diff --git a/.github/workflows/vfc_test_workflow.yml b/.github/workflows/vfc_test_workflow.yml
new file mode 100644
index 0000000..61bad51
--- /dev/null
+++ b/.github/workflows/vfc_test_workflow.yml
@@ -0,0 +1,57 @@
+# This workflow will be executed when dev is updated:
+# it will run the configured tests and upload the results on vfc_ci_dev.
+
+name: "Verificarlo CI (dev)"
+
+on:
+ # Triggers the workflow when dev is updated
+ push:
+ branches: [ dev ]
+
+ workflow_dispatch:
+
+
+jobs:
+ run_verificarlo_tests:
+ runs-on: ubuntu-latest
+ container: verificarlo/verificarlo
+
+ steps:
+ - uses: actions/checkout@v2
+ with:
+ fetch-depth: 0
+
+ # We will probably drop these installations when integrating CI into
+ # Verificarlo
+ - name: Install Python requirements
+ run: |
+ pip install numpy scipy pandas bokeh jinja2 tables GitPython
+ apt update
+ apt install -y wget libhdf5-dev g++
+ wget https://raw.githubusercontent.com/verificarlo/significantdigits/main/sigdigits.py -P /usr/local/lib/python3.8/dist-packages
+
+ - name: Run tests
+ # We assume the script is included in the repo for now
+ # (we'll probably want to remove "./" if the script ends up being integrated
+ # in Verificarlo and becomes available system-wide)
+ run: ./vfc_ci test -g -r
+
+ - name: Commit test results
+ run: |
+ git_hash=$(git rev-parse --short "$GITHUB_SHA")
+
+ git config --local user.email "action@github.com"
+ git config --local user.name "GitHub Action"
+
+ git checkout vfc_ci_dev
+ mkdir -p vfcruns
+ mv *.vfcrun.h5 vfcruns
+ git add vfcruns/*
+ git commit -m "[auto] New test results for commit ${git_hash}"
+ git push
+
+ - name: Upload raw results as artifacts
+ uses: actions/upload-artifact@v2
+ with:
+ name: ${{github.sha}}.vfcraw
+ path: ./*.vfcraw.h5
diff --git a/.gitignore b/.gitignore
index 9980d03..f372432 100644
--- a/.gitignore
+++ b/.gitignore
@@ -10,3 +10,8 @@ Slater*
Updates*
datasets/dataset.*
bin/
+*.vfcrun.hd5
+*.vfcraw.hd5
+__pycache__
+ci/__pycache__
+*.h5
diff --git a/Makefile.verificarlo b/Makefile.verificarlo
index 167b4b2..bd10702 100644
--- a/Makefile.verificarlo
+++ b/Makefile.verificarlo
@@ -33,6 +33,7 @@ BIN_DIR := bin
EXEC := $(BIN_DIR)/cMaponiA3_test_3x3_3 \
$(BIN_DIR)/test_h5 \
+ $(BIN_DIR)/vfc_test_h5 \
$(BIN_DIR)/fMaponiA3_test_3x3_3 \
$(BIN_DIR)/fMaponiA3_test_4x4_2 \
$(BIN_DIR)/QMCChem_dataset_test
@@ -84,6 +85,9 @@ $(BIN_DIR)/cMaponiA3_test_3x3_3: $(OBJ_DIR)/cMaponiA3_test_3x3_3.o $(DEPS_CXX) |
$(BIN_DIR)/test_h5: $(OBJ_DIR)/test_h5.o $(DEPS_CXX) | $(BIN_DIR)
$(CXX) -o $@ $^ $(H5FLAGS)
+$(BIN_DIR)/vfc_test_h5: $(OBJ_DIR)/vfc_test_h5.o $(DEPS_CXX) | $(BIN_DIR)
+ $(CXX) -o $@ $^ $(H5FLAGS)
+
$(BIN_DIR)/fMaponiA3_test_3x3_3: $(DEPS_F) $(OBJ_DIR)/fMaponiA3_test_3x3_3.o | $(BIN_DIR)
$(FC) $(FLIBS) -o $@ $^
@@ -92,5 +96,3 @@ $(BIN_DIR)/fMaponiA3_test_4x4_2: $(DEPS_F) $(OBJ_DIR)/fMaponiA3_test_4x4_2.o |
$(BIN_DIR)/QMCChem_dataset_test: $(DEPS_F) $(OBJ_DIR)/QMCChem_dataset_test.o | $(BIN_DIR)
$(FC) $(FLIBS) -o $@ $^
-
-
diff --git a/ci/__init__.py b/ci/__init__.py
new file mode 100644
index 0000000..e69de29
diff --git a/ci/serve.py b/ci/serve.py
new file mode 100755
index 0000000..37d91f2
--- /dev/null
+++ b/ci/serve.py
@@ -0,0 +1,28 @@
+# Server for the Verificarlo CI report. This is simply a wrapper to avoid
+# calling Bokeh directly.
+
+import os
+
+
+def serve(show, git_directory, git_url, port, allow_origin, logo_url):
+
+ # Prepare arguments
+ show = "--show" if show else ""
+
+ git = ""
+ if git_directory is not None:
+ git = "git directory %s" % git_directory
+ if git_url is not None:
+ git = "git url %s" % git_url
+
+ logo = ""
+ if logo_url is not None:
+ logo = "logo %s" % logo_url
+
+ dirname = os.path.dirname(__file__)
+
+ # Call the "bokeh serve" command on the system
+ command = "bokeh serve %s/vfc_ci_report %s --allow-websocket-origin=%s:%s --port %s --args %s %s" \
+ % (dirname, show, allow_origin, port, port, git, logo)
+
+ os.system(command)
diff --git a/ci/setup.py b/ci/setup.py
new file mode 100644
index 0000000..1bd50b3
--- /dev/null
+++ b/ci/setup.py
@@ -0,0 +1,146 @@
+# Helper script to set up Verificarlo CI on the current branch
+
+import git
+
+import sys
+import os
+from jinja2 import Environment, FileSystemLoader
+
+##########################################################################
+
+# Helper functions
+
+
+def gen_readme(dev_branch, ci_branch):
+
+ # Init template loader
+ path = os.path.dirname(os.path.abspath(__file__))
+ env = Environment(loader=FileSystemLoader(path))
+ template = env.get_template("workflow_templates/ci_README.j2.md")
+
+ # Render template
+ render = template.render(dev_branch=dev_branch, ci_branch=ci_branch)
+
+ # Write template
+ with open("README.md", "w") as fh:
+ fh.write(render)
+
+
+def gen_workflow(git_host, dev_branch, ci_branch, repo):
+
+ # Init template loader
+ path = os.path.dirname(os.path.abspath(__file__))
+ env = Environment(loader=FileSystemLoader(path))
+
+ if git_host == "github":
+ # Load template
+ template = env.get_template(
+ "workflow_templates/vfc_test_workflow.j2.yml")
+
+ # Render it
+ render = template.render(dev_branch=dev_branch, ci_branch=ci_branch)
+
+ # Write the file
+ filename = ".github/workflows/vfc_test_workflow.yml"
+ os.makedirs(os.path.dirname(filename), exist_ok=True)
+ with open(filename, "w") as fh:
+ fh.write(render)
+
+ if git_host == "gitlab":
+ template = env.get_template("workflow_templates/gitlab-ci.j2.yml")
+
+ # Ask for the user who will run the jobs (Gitlab specific)
+ username = input(
+ "[vfc_ci] Enter the name of the user who will run the CI jobs:")
+ email = input(
+ "[vfc_ci] Enter the e-mail of the user who will run the CI jobs:")
+
+ remote_url = repo.remotes[0].config_reader.get("url")
+ remote_url = remote_url.replace("http://", "")
+ remote_url = remote_url.replace("https://", "")
+
+ render = template.render(
+ dev_branch=dev_branch,
+ ci_branch=ci_branch,
+ username=username,
+ email=email,
+ remote_url=remote_url
+ )
+
+ filename = ".gitlab-ci.yml"
+ with open(filename, "w") as fh:
+ fh.write(render)
+
+
+##########################################################################
+
+def setup(git_host):
+
+ # Init repo and make sure that the workflow setup is possible
+
+ repo = git.Repo(".")
+ repo.remotes.origin.fetch()
+
+ # Make sure that repository is clean
+ assert(not repo.is_dirty()), "Error [vfc_ci]: Unstaged changes detected " \
+ "in your work tree."
+
+ dev_branch = repo.active_branch
+ dev_branch_name = str(dev_branch)
+ dev_remote = dev_branch.tracking_branch()
+
+ # Make sure that the active branch (on which to setup the workflow) has a
+ # remote
+ assert(dev_remote is not None), "Error [vfc_ci]: The current branch doesn't " \
+ "have a remote."
+
+ # Make sure that we are not behind the remote (so we can push safely later)
+ rev = "%s...%s" % (dev_branch_name, str(dev_remote))
+ commits_behind = list(repo.iter_commits(rev))
+ assert(commits_behind == []), "Error [vfc_ci]: The local branch seems " \
+ "to be at least one commit behind remote."
+
+ # Commit the workflow on the current (dev) branch
+
+ ci_branch_name = "vfc_ci_%s" % dev_branch_name
+ gen_workflow(git_host, dev_branch_name, ci_branch_name, repo)
+ repo.git.add(".")
+ repo.index.commit("[auto] Set up Verificarlo CI on this branch")
+ repo.remote(name="origin").push()
+
+ # Create the CI branch (orphan branch with a readme on it)
+ # (see : https://github.com/gitpython-developers/GitPython/issues/615)
+
+ repo.head.reference = git.Head(repo, "refs/heads/" + ci_branch_name)
+
+ repo.index.remove(["*"])
+ gen_readme(dev_branch_name, ci_branch_name)
+ repo.index.add(["README.md"])
+
+ repo.index.commit(
+ "[auto] Create the Verificarlo CI branch for %s" % dev_branch_name,
+ parent_commits=None
+ )
+ repo.remote(name="origin").push(
+ refspec="%s:%s" % (ci_branch_name, ci_branch_name)
+ )
+
+ # Force checkout back to the original (dev) branch
+ repo.git.checkout(dev_branch_name, force=True)
+
+ # Print termination messages
+
+ print(
+ "Info [vfc_ci]: A Verificarlo CI workflow has been setup on "
+ "%s." % dev_branch_name
+ )
+ print(
+ "Info [vfc_ci]: Make sure that you have a \"vfc_tests_config.json\" on "
+ "this branch. You can also perform a \"vfc_ci test\" dry run before "
+ "pushing other commits.")
+
+ if git_host == "gitlab":
+ print(
+ "Info [vfc_ci]: Since you are using GitLab, make sure that you "
+ "have created an access token for the user you specified (registered "
+ "as a variable called \"CI_PUSH_TOKEN\" in your repository).")
diff --git a/ci/test.py b/ci/test.py
new file mode 100755
index 0000000..bc38714
--- /dev/null
+++ b/ci/test.py
@@ -0,0 +1,367 @@
+# This script reads the vfc_tests_config.json file and executes tests accordingly
+# It will also generate a ... .vfcrunh5 file with the results of the run
+
+import sigdigits as sd
+import scipy.stats
+import numpy as np
+import pandas as pd
+import os
+import json
+
+import calendar
+import time
+
+# Forcing an older pickle protocol allows backwards compatibility when reading
+# HDF5 written in 3.8+ using an older version of Python
+import pickle
+pickle.HIGHEST_PROTOCOL = 4
+
+
+# Magic numbers
+min_pvalue = 0.05
+max_zscore = 3
+
+
+##########################################################################
+
+# Helper functions
+
+# Read a CSV file outputted by vfc_probe as a Pandas dataframe
+def read_probes_csv(filepath, backend, warnings, execution_data):
+
+ try:
+ results = pd.read_csv(filepath)
+
+ except FileNotFoundError:
+ print(
+ "Warning [vfc_ci]: Probes not found, your code might have crashed "
+ "or you might have forgotten to call vfc_dump_probes"
+ )
+ warnings.append(execution_data)
+ return pd.DataFrame(
+ columns=["test", "variable", "values", "vfc_backend"]
+ )
+
+ except Exception:
+ print(
+ "Warning [vfc_ci]: Your probes could not be read for some unknown "
+ "reason"
+ )
+ warnings.append(execution_data)
+ return pd.DataFrame(
+ columns=["test", "variable", "values", "vfc_backend"]
+ )
+
+ if len(results) == 0:
+ print(
+ "Warning [vfc_ci]: Probes empty, it looks like you have dumped "
+ "them without calling vfc_put_probe"
+ )
+ warnings.append(execution_data)
+
+ # Once the CSV has been opened and validated, return its content
+ results["value"] = results["value"].apply(lambda x: float.fromhex(x))
+ results.rename(columns={"value": "values"}, inplace=True)
+
+ results["vfc_backend"] = backend
+
+ return results
+
+
+# Wrappers to sd.significant_digits (returns results in base 2)
+
+def significant_digits(x):
+
+ # If the null hypothesis is rejected, call sigdigits with the General
+ # formula:
+ if x.pvalue < min_pvalue:
+ # In a pandas DF, "values" actually refers to the array of columns, and
+ # not the column named "values"
+ distribution = x.values[3]
+ distribution = distribution.reshape(len(distribution), 1)
+
+ # The distribution's empirical average will be used as the reference
+ mu = np.array([x.mu])
+
+ s = sd.significant_digits(
+ distribution,
+ mu,
+ precision=sd.Precision.Relative,
+ method=sd.Method.General,
+
+ probability=0.9,
+ confidence=0.95
+ )
+
+ # s is returned inside a list
+ return s[0]
+
+ # Else, manually compute sMCA (Stott-Parker formula)
+ else:
+ return -np.log2(np.absolute(x.sigma / x.mu))
+
+
+def significant_digits_lower_bound(x):
+ # If the null hypothesis is rejected, no lower bound
+ if x.pvalue < min_pvalue:
+ return x.s2
+
+ # Else, the lower bound will be computed with p= .9 alpha-1=.95
+ else:
+ distribution = x.values[3]
+ distribution = distribution.reshape(len(distribution), 1)
+
+ mu = np.array([x.mu])
+
+ s = sd.significant_digits(
+ distribution,
+ mu,
+ precision=sd.Precision.Relative,
+ method=sd.Method.CNH,
+
+ probability=0.9,
+ confidence=0.95
+ )
+
+ return s[0]
+
+
+##########################################################################
+
+ # Main functions
+
+
+# Open and read the tests config file
+def read_config():
+ try:
+ with open("vfc_tests_config.json", "r") as file:
+ data = file.read()
+
+ except FileNotFoundError as e:
+ e.strerror = "Error [vfc_ci]: This file is required to describe the tests "\
+ "to run and generate a Verificarlo run file"
+ raise e
+
+ return json.loads(data)
+
+
+# Set up metadata
+def generate_metadata(is_git_commit):
+
+ # Metadata and filename are initiated as if no commit was associated
+ metadata = {
+ "timestamp": calendar.timegm(time.gmtime()),
+ "is_git_commit": is_git_commit,
+ "hash": "",
+ "author": "",
+ "message": ""
+ }
+
+ if is_git_commit:
+ print("Fetching metadata from last commit...")
+ from git import Repo
+
+ repo = Repo(".")
+ head_commit = repo.head.commit
+
+ metadata["timestamp"] = head_commit.authored_date
+
+ metadata["hash"] = str(head_commit)[0:7]
+ metadata["author"] = "%s <%s>" \
+ % (str(head_commit.author), head_commit.author.email)
+ metadata["message"] = head_commit.message.split("\n")[0]
+
+ return metadata
+
+
+# Execute tests and collect results in a Pandas dataframe (+ dataprocessing)
+def run_tests(config):
+
+ # Run the build command
+ print("Info [vfc_ci]: Building tests...")
+ os.system(config["make_command"])
+
+ # This is an array of Pandas dataframes for now
+ data = []
+
+ # Create tmp folder to export results
+ os.system("mkdir .vfcruns.tmp")
+ n_files = 0
+
+ # This will contain all executables/repetition numbers from which we could
+ # not get any data
+ warnings = []
+
+ # Tests execution loop
+ for executable in config["executables"]:
+ print("Info [vfc_ci]: Running executable :",
+ executable["executable"], "...")
+
+ parameters = ""
+ if "parameters" in executable:
+ parameters = executable["parameters"]
+
+ for backend in executable["vfc_backends"]:
+
+ export_backend = "VFC_BACKENDS=\"" + backend["name"] + "\" "
+ command = "./" + executable["executable"] + " " + parameters
+
+ repetitions = 1
+ if "repetitions" in backend:
+ repetitions = backend["repetitions"]
+
+ # Run test repetitions and save results
+ for i in range(repetitions):
+ file = ".vfcruns.tmp/%s.csv" % str(n_files)
+ export_output = "VFC_PROBES_OUTPUT=\"%s\" " % file
+ os.system(export_output + export_backend + command)
+
+ # This will only be used if we need to append this exec to the
+ # warnings list
+ execution_data = {
+ "executable": executable["executable"],
+ "backend": backend["name"],
+ "repetition": i + 1
+ }
+
+ data.append(read_probes_csv(
+ file,
+ backend["name"],
+ warnings,
+ execution_data
+ ))
+
+ n_files = n_files + 1
+
+ # Clean CSV output files (by deleting the tmp folder)
+ os.system("rm -rf .vfcruns.tmp")
+
+ # Combine all separate executions in one dataframe
+ data = pd.concat(data, sort=False, ignore_index=True)
+ data = data.groupby(["test", "vfc_backend", "variable"])\
+ .values.apply(list).reset_index()
+
+ # Make sure we have some data to work on
+ assert(len(data) != 0), "Error [vfc_ci]: No data have been generated " \
+ "by your tests executions, aborting run without writing results file"
+
+ return data, warnings
+
+ # Data processing
+
+
+def data_processing(data):
+
+ data["values"] = data["values"].apply(lambda x: np.array(x).astype(float))
+
+ # Get empirical average, standard deviation and p-value
+ data["mu"] = data["values"].apply(np.average)
+ data["sigma"] = data["values"].apply(np.std)
+ data["pvalue"] = data["values"].apply(
+ lambda x: scipy.stats.shapiro(x).pvalue)
+
+ # Significant digits
+ data["s2"] = data.apply(significant_digits, axis=1)
+ data["s10"] = data["s2"].apply(lambda x: sd.change_base(x, 10))
+
+ # Lower bound of the confidence interval using the sigdigits module
+ data["s2_lower_bound"] = data.apply(significant_digits_lower_bound, axis=1)
+ data["s10_lower_bound"] = data["s2_lower_bound"].apply(
+ lambda x: sd.change_base(x, 10))
+
+ # Compute moments of the distribution
+ # (including a new distribution obtained by filtering outliers)
+ data["values"] = data["values"].apply(np.sort)
+
+ data["mu"] = data["values"].apply(np.average)
+ data["min"] = data["values"].apply(np.min)
+ data["quantile25"] = data["values"].apply(np.quantile, args=(0.25,))
+ data["quantile50"] = data["values"].apply(np.quantile, args=(0.50,))
+ data["quantile75"] = data["values"].apply(np.quantile, args=(0.75,))
+ data["max"] = data["values"].apply(np.max)
+
+ data["nsamples"] = data["values"].apply(len)
+
+ # Display all executions that resulted in a warning
+
+
+def show_warnings(warnings):
+ if len(warnings) > 0:
+ print(
+ "Warning [vfc_ci]: Some of your runs could not generate any data "
+ "(for instance because your code crashed) and resulted in "
+ "warnings. Here is the complete list :"
+ )
+
+ for i in range(0, len(warnings)):
+ print("- Warning %s:" % i)
+
+ print(" Executable: %s" % warnings[i]["executable"])
+ print(" Backend: %s" % warnings[i]["backend"])
+ print(" Repetition: %s" % warnings[i]["repetition"])
+
+
+##########################################################################
+
+ # Entry point
+
+def run(is_git_commit, export_raw_values, dry_run):
+
+ # Get config, metadata and data
+ print("Info [vfc_ci]: Reading tests config file...")
+ config = read_config()
+
+ print("Info [vfc_ci]: Generating run metadata...")
+ metadata = generate_metadata(is_git_commit)
+
+ data, warnings = run_tests(config)
+ show_warnings(warnings)
+
+ # Data processing
+ print("Info [vfc_ci]: Processing data...")
+ data_processing(data)
+
+ # Prepare data for export (by creating a proper index and linking run
+ # timestamp)
+ data = data.set_index(["test", "variable", "vfc_backend"]).sort_index()
+ data["timestamp"] = metadata["timestamp"]
+
+ filename = metadata["hash"] if is_git_commit else str(
+ metadata["timestamp"])
+
+ # Prepare metadata for export
+ metadata = pd.DataFrame.from_dict([metadata])
+ metadata = metadata.set_index("timestamp")
+
+ # NOTE : Exporting to HDF5 requires to install "tables" on the system
+
+ # Export raw data if needed
+ if export_raw_values and not dry_run:
+ data.to_hdf(filename + ".vfcraw.h5", key="data")
+ metadata.to_hdf(filename + ".vfcraw.h5", key="metadata")
+
+ # Export data
+ del data["values"]
+ if not dry_run:
+ data.to_hdf(filename + ".vfcrun.h5", key="data")
+ metadata.to_hdf(filename + ".vfcrun.h5", key="metadata")
+
+ # Print termination messages
+ print(
+ "Info [vfc_ci]: The results have been successfully written to "
+ "%s.vfcrun.h5."
+ % filename
+ )
+
+ if export_raw_values:
+ print(
+ "Info [vfc_ci]: A file containing the raw values has also been "
+ "created : %s.vfcraw.h5."
+ % filename
+ )
+
+ if dry_run:
+ print(
+ "Info [vfc_ci]: The dry run flag was enabled, so no files were "
+ "actually created."
+ )
diff --git a/ci/vfc_ci_report/compare_runs.py b/ci/vfc_ci_report/compare_runs.py
new file mode 100644
index 0000000..bc8da4e
--- /dev/null
+++ b/ci/vfc_ci_report/compare_runs.py
@@ -0,0 +1,542 @@
+# Manage the view comparing a variable over different runs
+
+import time
+
+import pandas as pd
+
+from math import pi
+
+from bokeh.plotting import figure, curdoc
+from bokeh.embed import components
+from bokeh.models import Select, ColumnDataSource, Panel, Tabs, HoverTool, \
+ TextInput, CheckboxGroup, TapTool, CustomJS
+
+import helper
+import plot
+
+
+##########################################################################
+
+
+class CompareRuns:
+
+ # Helper functions related to CompareRuns
+
+ # From an array of timestamps, returns the array of runs names (for the x
+ # axis ticks), as well as the metadata (in a dict of arrays) associated to
+ # this array (for the tooltips)
+ def gen_x_series(self, timestamps):
+
+ # Initialize the objects to return
+ x_series = []
+ x_metadata = dict(
+ date=[],
+ is_git_commit=[],
+ hash=[],
+ author=[],
+ message=[]
+ )
+
+ # n == 0 means we want all runs, we also make sure not to go out of
+ # bound if asked for more runs than we have
+ n = self.current_n_runs
+ if n == 0 or n > len(timestamps):
+ n = len(timestamps)
+
+ for i in range(0, n):
+ # Get metadata associated to this run
+ row_metadata = helper.get_metadata(
+ self.metadata, timestamps[-i - 1])
+ date = time.ctime(timestamps[-i - 1])
+
+ # Fill the x series
+ str = row_metadata["name"]
+ x_series.insert(0, helper.get_metadata(
+ self.metadata, timestamps[-i - 1])["name"])
+
+ # Fill the metadata lists
+ x_metadata["date"].insert(0, date)
+ x_metadata["is_git_commit"].insert(
+ 0, row_metadata["is_git_commit"])
+ x_metadata["hash"].insert(0, row_metadata["hash"])
+ x_metadata["author"].insert(0, row_metadata["author"])
+ x_metadata["message"].insert(0, row_metadata["message"])
+
+ return x_series, x_metadata
+
+ # Plots update function
+
+ def update_plots(self):
+
+ # Select all data matching current test/var/backend
+
+ runs = self.data.loc[[self.widgets["select_test"].value],
+ self.widgets["select_var"].value,
+ self.widgets["select_backend"].value]
+
+ timestamps = runs["timestamp"]
+ x_series, x_metadata = self.gen_x_series(timestamps.sort_values())
+
+ # Update source
+
+ main_dict = runs.to_dict("series")
+ main_dict["x"] = x_series
+
+ # Add metadata (for tooltip)
+ main_dict.update(x_metadata)
+
+ # Select the last n runs only
+ n = self.current_n_runs
+ main_dict = {key: value[-n:] for key, value in main_dict.items()}
+
+ # Generate ColumnDataSources for the 3 dotplots
+ for stat in ["sigma", "s10", "s2"]:
+ dict = {
+ "%s_x" % stat: main_dict["x"],
+
+ "is_git_commit": main_dict["is_git_commit"],
+ "date": main_dict["date"],
+ "hash": main_dict["hash"],
+ "author": main_dict["author"],
+ "message": main_dict["message"],
+
+ stat: main_dict[stat],
+
+ "nsamples": main_dict["nsamples"],
+ }
+
+ if stat == "s10" or stat == "s2":
+ dict["%s_lower_bound" %
+ stat] = main_dict["%s_lower_bound" %
+ stat]
+
+ # Filter outliers if the box is checked
+ if len(self.widgets["outliers_filtering_compare"].active) > 0:
+ outliers = helper.detect_outliers(dict[stat])
+ dict[stat] = helper.remove_outliers(dict[stat], outliers)
+ dict["%s_x" % stat] = helper.remove_outliers(
+ dict["%s_x" % stat], outliers)
+
+ # Assign ColumnDataSource
+ self.sources["%s_source" % stat].data = dict
+
+ # Generate ColumnDataSource for the boxplot
+ dict = {
+ "is_git_commit": main_dict["is_git_commit"],
+ "date": main_dict["date"],
+ "hash": main_dict["hash"],
+ "author": main_dict["author"],
+ "message": main_dict["message"],
+
+ "x": main_dict["x"],
+ "min": main_dict["min"],
+ "quantile25": main_dict["quantile25"],
+ "quantile50": main_dict["quantile50"],
+ "quantile75": main_dict["quantile75"],
+ "max": main_dict["max"],
+ "mu": main_dict["mu"],
+ "pvalue": main_dict["pvalue"],
+
+ "nsamples": main_dict["nsamples"]
+ }
+
+ self.sources["boxplot_source"].data = dict
+
+ # Update x axis
+
+ helper.reset_x_range(
+ self.plots["boxplot"],
+ self.sources["boxplot_source"].data["x"]
+ )
+ helper.reset_x_range(
+ self.plots["sigma_plot"],
+ self.sources["sigma_source"].data["sigma_x"]
+ )
+ helper.reset_x_range(
+ self.plots["s10_plot"],
+ self.sources["s10_source"].data["s10_x"]
+ )
+ helper.reset_x_range(
+ self.plots["s2_plot"],
+ self.sources["s2_source"].data["s2_x"]
+ )
+
+ # Widgets' callback functions
+
+ def update_test(self, attrname, old, new):
+
+ # If the value is updated by the CustomJS, self.widgets["select_var"].value
+ # won't be updated, so we have to look for that case and assign it
+ # manually
+
+ # "new" should be a list when updated by CustomJS
+ if isinstance(new, list):
+ # If filtering removed all options, we might have an empty list
+ # (in this case, we just skip the callback and do nothing)
+ if len(new) > 0:
+ new = new[0]
+ else:
+ return
+
+ if new != self.widgets["select_test"].value:
+ # The callback will be triggered again with the updated value
+ self.widgets["select_test"].value = new
+ return
+
+ # New list of available vars
+ self.vars = self.data.loc[new]\
+ .index.get_level_values("variable").drop_duplicates().tolist()
+ self.widgets["select_var"].options = self.vars
+
+ # Reset var selection if old one is not available in new vars
+ if self.widgets["select_var"].value not in self.vars:
+ self.widgets["select_var"].value = self.vars[0]
+ # The update_var callback will be triggered by the assignment
+
+ else:
+ # Trigger the callback manually (since the plots need to be updated
+ # anyway)
+ self.update_var("", "", self.widgets["select_var"].value)
+
+ def update_var(self, attrname, old, new):
+
+ # If the value is updated by the CustomJS, self.widgets["select_var"].value
+ # won't be updated, so we have to look for that case and assign it
+ # manually
+
+ # new should be a list when updated by CustomJS
+ if isinstance(new, list):
+ new = new[0]
+
+ if new != self.widgets["select_var"].value:
+ # The callback will be triggered again with the updated value
+ self.widgets["select_var"].value = new
+ return
+
+ # New list of available backends
+ self.backends = self.data.loc[self.widgets["select_test"].value, self.widgets["select_var"].value]\
+ .index.get_level_values("vfc_backend").drop_duplicates().tolist()
+ self.widgets["select_backend"].options = self.backends
+
+ # Reset backend selection if old one is not available in new backends
+ if self.widgets["select_backend"].value not in self.backends:
+ self.widgets["select_backend"].value = self.backends[0]
+ # The update_backend callback will be triggered by the assignment
+
+ else:
+ # Trigger the callback manually (since the plots need to be updated
+ # anyway)
+ self.update_backend("", "", self.widgets["select_backend"].value)
+
+ def update_backend(self, attrname, old, new):
+
+ # Simply update plots, since no other data is affected
+ self.update_plots()
+
+ def update_n_runs(self, attrname, old, new):
+ # Simply update runs selection (value and string display)
+ self.select_n_runs.value = new
+ self.current_n_runs = self.n_runs_dict[self.select_n_runs.value]
+
+ self.update_plots()
+
+ def update_outliers_filtering(self, attrname, old, new):
+ self.update_plots()
+
+ # Bokeh setup functions
+
+ def setup_plots(self):
+
+ tools = "pan, wheel_zoom, xwheel_zoom, ywheel_zoom, reset, save"
+
+ # Custom JS callback that will be used when tapping on a run
+ # Only switches the view, a server callback is required to update plots
+ # (defined inside template to avoid bloating server w/ too much JS code)
+ js_tap_callback = "goToInspectRuns();"
+
+ # Box plot
+ self.plots["boxplot"] = figure(
+ name="boxplot", title="Variable distribution over runs",
+ plot_width=900, plot_height=400, x_range=[""],
+ tools=tools, sizing_mode="scale_width"
+ )
+
+ box_tooltips = [
+ ("Git commit", "@is_git_commit"),
+ ("Date", "@date"),
+ ("Hash", "@hash"),
+ ("Author", "@author"),
+ ("Message", "@message"),
+ ("Min", "@min{%0.18e}"),
+ ("Max", "@max{%0.18e}"),
+ ("1st quartile", "@quantile25{%0.18e}"),
+ ("Median", "@quantile50{%0.18e}"),
+ ("3rd quartile", "@quantile75{%0.18e}"),
+ ("μ", "@mu{%0.18e}"),
+ ("p-value", "@pvalue"),
+ ("Number of samples", "@nsamples")
+ ]
+ box_tooltips_formatters = {
+ "@min": "printf",
+ "@max": "printf",
+ "@quantile25": "printf",
+ "@quantile50": "printf",
+ "@quantile75": "printf",
+ "@mu": "printf"
+ }
+
+ plot.fill_boxplot(
+ self.plots["boxplot"], self.sources["boxplot_source"],
+ tooltips=box_tooltips,
+ tooltips_formatters=box_tooltips_formatters,
+ js_tap_callback=js_tap_callback,
+ server_tap_callback=self.inspect_run_callback_boxplot,
+ )
+ self.doc.add_root(self.plots["boxplot"])
+
+ # Sigma plot (bar plot)
+ self.plots["sigma_plot"] = figure(
+ name="sigma_plot", title="Standard deviation σ over runs",
+ plot_width=900, plot_height=400, x_range=[""],
+ tools=tools, sizing_mode="scale_width"
+ )
+
+ sigma_tooltips = [
+ ("Git commit", "@is_git_commit"),
+ ("Date", "@date"),
+ ("Hash", "@hash"),
+ ("Author", "@author"),
+ ("Message", "@message"),
+ ("σ", "@sigma"),
+ ("Number of samples", "@nsamples")
+ ]
+
+ plot.fill_dotplot(
+ self.plots["sigma_plot"], self.sources["sigma_source"], "sigma",
+ tooltips=sigma_tooltips,
+ js_tap_callback=js_tap_callback,
+ server_tap_callback=self.inspect_run_callback_sigma,
+ lines=True
+ )
+ self.doc.add_root(self.plots["sigma_plot"])
+
+ # s plot (bar plot with 2 tabs)
+ self.plots["s10_plot"] = figure(
+ name="s10_plot", title="Significant digits s over runs",
+ plot_width=900, plot_height=400, x_range=[""],
+ tools=tools, sizing_mode="scale_width"
+ )
+
+ s10_tooltips = [
+ ("Git commit", "@is_git_commit"),
+ ("Date", "@date"),
+ ("Hash", "@hash"),
+ ("Author", "@author"),
+ ("Message", "@message"),
+ ("s", "@s10"),
+ ("s lower bound", "@s10_lower_bound"),
+ ("Number of samples", "@nsamples")
+ ]
+
+ plot.fill_dotplot(
+ self.plots["s10_plot"], self.sources["s10_source"], "s10",
+ tooltips=s10_tooltips,
+ js_tap_callback=js_tap_callback,
+ server_tap_callback=self.inspect_run_callback_s10,
+ lines=True,
+ lower_bound=True
+ )
+ s10_tab = Panel(child=self.plots["s10_plot"], title="Base 10")
+
+ self.plots["s2_plot"] = figure(
+ name="s2_plot", title="Significant digits s over runs",
+ plot_width=900, plot_height=400, x_range=[""],
+ tools=tools, sizing_mode="scale_width"
+ )
+
+ s2_tooltips = [
+ ("Git commit", "@is_git_commit"),
+ ("Date", "@date"),
+ ("Hash", "@hash"),
+ ("Author", "@author"),
+ ("Message", "@message"),
+ ("s", "@s2"),
+ ("s lower bound", "@s2_lower_bound"),
+ ("Number of samples", "@nsamples")
+ ]
+
+ plot.fill_dotplot(
+ self.plots["s2_plot"], self.sources["s2_source"], "s2",
+ tooltips=s2_tooltips,
+ js_tap_callback=js_tap_callback,
+ server_tap_callback=self.inspect_run_callback_s2,
+ lines=True,
+ lower_bound=True
+ )
+ s2_tab = Panel(child=self.plots["s2_plot"], title="Base 2")
+
+ s_tabs = Tabs(
+ name="s_tabs",
+ tabs=[s10_tab, s2_tab],
+ tabs_location="below"
+ )
+
+ self.doc.add_root(s_tabs)
+
+ def setup_widgets(self):
+
+ # Initial selections
+
+ # Test/var/backend combination (we select all first elements at init)
+ self.tests = self.data\
+ .index.get_level_values("test").drop_duplicates().tolist()
+
+ self.vars = self.data.loc[self.tests[0]]\
+ .index.get_level_values("variable").drop_duplicates().tolist()
+
+ self.backends = self.data.loc[self.tests[0], self.vars[0]]\
+ .index.get_level_values("vfc_backend").drop_duplicates().tolist()
+
+ # Custom JS callback that will be used client side to filter selections
+ filter_callback_js = """
+ selector.options = options.filter(e => e.includes(cb_obj.value));
+ """
+
+ # Test selector widget
+
+ # Number of runs to display
+ # The dict structure allows us to get int value from the display string
+ # in O(1)
+ self.n_runs_dict = {
+ "Last 3 runs": 3,
+ "Last 5 runs": 5,
+ "Last 10 runs": 10,
+ "All runs": 0
+ }
+
+ # Contains all options strings
+ n_runs_display = list(self.n_runs_dict.keys())
+
+ # Will be used when updating plots (contains actual number to diplay)
+ self.current_n_runs = self.n_runs_dict[n_runs_display[1]]
+
+ # Selector widget
+ self.widgets["select_test"] = Select(
+ name="select_test", title="Test :",
+ value=self.tests[0], options=self.tests
+ )
+ self.doc.add_root(self.widgets["select_test"])
+ self.widgets["select_test"].on_change("value", self.update_test)
+ self.widgets["select_test"].on_change("options", self.update_test)
+
+ # Filter widget
+ self.widgets["test_filter"] = TextInput(
+ name="test_filter", title="Tests filter:"
+ )
+ self.widgets["test_filter"].js_on_change(
+ "value",
+ CustomJS(
+ args=dict(
+ options=self.tests,
+ selector=self.widgets["select_test"]),
+ code=filter_callback_js))
+ self.doc.add_root(self.widgets["test_filter"])
+
+ # Number of runs to display
+
+ self.widgets["select_n_runs"] = Select(
+ name="select_n_runs", title="Display :",
+ value=n_runs_display[1], options=n_runs_display
+ )
+ self.doc.add_root(self.widgets["select_n_runs"])
+ self.widgets["select_n_runs"].on_change("value", self.update_n_runs)
+
+ # Variable selector widget
+
+ self.widgets["select_var"] = Select(
+ name="select_var", title="Variable :",
+ value=self.vars[0], options=self.vars
+ )
+ self.doc.add_root(self.widgets["select_var"])
+ self.widgets["select_var"].on_change("value", self.update_var)
+ self.widgets["select_var"].on_change("options", self.update_var)
+
+ # Backend selector widget
+
+ self.widgets["select_backend"] = Select(
+ name="select_backend", title="Verificarlo backend :",
+ value=self.backends[0], options=self.backends
+ )
+ self.doc.add_root(self.widgets["select_backend"])
+ self.widgets["select_backend"].on_change("value", self.update_backend)
+
+ # Outliers filtering checkbox
+
+ self.widgets["outliers_filtering_compare"] = CheckboxGroup(
+ name="outliers_filtering_compare",
+ labels=["Filter outliers"], active=[]
+ )
+ self.doc.add_root(self.widgets["outliers_filtering_compare"])
+ self.widgets["outliers_filtering_compare"]\
+ .on_change("active", self.update_outliers_filtering)
+
+ # Communication methods
+ # (to send/receive messages to/from master)
+
+ # Callback to change view of Inspect runs when data is selected
+
+ def inspect_run_callback(self, new, source_name, x_name):
+
+ # In case we just unselected everything, then do nothing
+ if new == []:
+ return
+
+ index = new[-1]
+ run_name = self.sources[source_name].data[x_name][index]
+
+ self.master.go_to_inspect(run_name)
+
+ # Wrappers for each plot (since new is the index of the clicked element,
+ # it is dependent of the plot because we could have filtered some outliers)
+ # There doesn't seem to be an easy way to add custom parameters to a
+ # Bokeh callback, so using wrappers seems to be the best solution for now
+
+ def inspect_run_callback_boxplot(self, attr, old, new):
+ self.inspect_run_callback(new, "boxplot_source", "x")
+
+ def inspect_run_callback_sigma(self, attr, old, new):
+ self.inspect_run_callback(new, "sigma_source", "sigma_x")
+
+ def inspect_run_callback_s2(self, attr, old, new):
+ self.inspect_run_callback(new, "s2_source", "s2_x")
+
+ def inspect_run_callback_s10(self, attr, old, new):
+ self.inspect_run_callback(new, "s10_source", "s10_x")
+
+ # Constructor
+
+ def __init__(self, master, doc, data, metadata):
+
+ self.master = master
+
+ self.doc = doc
+ self.data = data
+ self.metadata = metadata
+
+ self.sources = {
+ "boxplot_source": ColumnDataSource(data={}),
+ "sigma_source": ColumnDataSource(data={}),
+ "s10_source": ColumnDataSource(data={}),
+ "s2_source": ColumnDataSource(data={})
+ }
+
+ self.plots = {}
+ self.widgets = {}
+
+ # Setup Bokeh objects
+ self.setup_plots()
+ self.setup_widgets()
+
+ # At this point, everything should have been initialized, so we can
+ # show the plots for the first time
+ self.update_plots()
diff --git a/ci/vfc_ci_report/helper.py b/ci/vfc_ci_report/helper.py
new file mode 100644
index 0000000..f258959
--- /dev/null
+++ b/ci/vfc_ci_report/helper.py
@@ -0,0 +1,170 @@
+# General helper functions for both compare_runs and compare_variables
+
+import calendar
+import time
+from itertools import compress
+
+import numpy as np
+
+# Magic numbers
+max_ticks = 15
+max_zscore = 3
+
+##########################################################################
+
+
+# From a timestamp, return the associated metadata as a Pandas serie
+def get_metadata(metadata, timestamp):
+ return metadata.loc[timestamp]
+
+
+# Convert a metadata Pandas series to a JS readable dict
+def metadata_to_dict(metadata):
+ dict = metadata.to_dict()
+
+ # JS doesn't accept True for booleans, and Python doesn't accept true
+ # (because of the caps) => using an integer is a portable solution
+ dict["is_git_commit"] = 1 if dict["is_git_commit"] else 0
+
+ dict["date"] = time.ctime(metadata.name)
+
+ return dict
+
+
+# Return a string that indicates the elapsed time since the run, used as the
+# x-axis tick in "Compare runs" or when selecting run in "Inspect run"
+def get_run_name(timestamp, hash):
+
+ gmt = time.gmtime()
+ now = calendar.timegm(gmt)
+ diff = now - timestamp
+
+ # Special case : < 1 minute (return string directly)
+ if diff < 60:
+ str = "Less than a minute ago"
+
+ if hash != "":
+ str = str + " (%s)" % hash
+
+ if str == get_run_name.previous:
+ get_run_name.counter = get_run_name.counter + 1
+ str = "%s (%s)" % (str, get_run_name.counter)
+ else:
+ get_run_name.counter = 0
+ get_run_name.previous = str
+
+ return str
+
+ # < 1 hour
+ if diff < 3600:
+ n = int(diff / 60)
+ str = "%s minute%s ago"
+ # < 1 day
+ elif diff < 86400:
+ n = int(diff / 3600)
+ str = "%s hour%s ago"
+ # < 1 week
+ elif diff < 604800:
+ n = int(diff / 86400)
+ str = "%s day%s ago"
+ # < 1 month
+ elif diff < 2592000:
+ n = int(diff / 604800)
+ str = "%s week%s ago"
+ # > 1 month
+ else:
+ n = diff / 2592000
+ str = "%s month%s ago"
+
+ plural = ""
+ if n != 1:
+ plural = "s"
+
+ str = str % (n, plural)
+
+ # We might want to add the git hash
+ if hash != "":
+ str = str + " (%s)" % hash
+
+ # Finally, check for duplicate with previously generated string
+ if str == get_run_name.previous:
+ # Increment the duplicate counter and add it to str
+ get_run_name.counter = get_run_name.counter + 1
+ str = "%s (%s)" % (str, get_run_name.counter)
+
+ else:
+ # No duplicate, reset both previously generated str and duplicate
+ # counter
+ get_run_name.counter = 0
+ get_run_name.previous = str
+
+ return str
+
+
+# These external variables will store data about the last generated string to
+# avoid duplicates (assuming the runs are sorted by time)
+get_run_name.counter = 0
+get_run_name.previous = ""
+
+
+def reset_run_strings():
+ get_run_name.counter = 0
+ get_run_name.previous = ""
+
+
+# Update all the x-ranges from a dict of plots
+def reset_x_range(plot, x_range):
+ plot.x_range.factors = x_range
+
+ if len(x_range) < max_ticks:
+ plot.xaxis.major_tick_line_color = "#000000"
+ plot.xaxis.minor_tick_line_color = "#000000"
+
+ plot.xaxis.major_label_text_font_size = "8pt"
+
+ else:
+ plot.xaxis.major_tick_line_color = None
+ plot.xaxis.minor_tick_line_color = None
+
+ plot.xaxis.major_label_text_font_size = "0pt"
+
+
+# Return an array of booleans that indicate which elements are outliers
+# (True means element is not an outlier and must be kept)
+def detect_outliers(array, max_zscore=max_zscore):
+ if len(array) <= 2:
+ return [True] * len(array)
+
+ median = np.median(array)
+ std = np.std(array)
+ if std == 0:
+ return array
+ distance = abs(array - median)
+ # Array of booleans with elements to be filtered
+ outliers_array = distance < max_zscore * std
+
+ return outliers_array
+
+
+def remove_outliers(array, outliers):
+ return list(compress(array, outliers))
+
+
+def remove_boxplot_outliers(dict, outliers, prefix):
+ outliers = detect_outliers(dict["%s_max" % prefix])
+
+ dict["%s_x" % prefix] = remove_outliers(dict["%s_x" % prefix], outliers)
+
+ dict["%s_min" % prefix] = remove_outliers(
+ dict["%s_min" % prefix], outliers)
+ dict["%s_quantile25" % prefix] = remove_outliers(
+ dict["%s_quantile25" % prefix], outliers)
+ dict["%s_quantile50" % prefix] = remove_outliers(
+ dict["%s_quantile50" % prefix], outliers)
+ dict["%s_quantile75" % prefix] = remove_outliers(
+ dict["%s_quantile75" % prefix], outliers)
+ dict["%s_max" % prefix] = remove_outliers(
+ dict["%s_max" % prefix], outliers)
+ dict["%s_mu" % prefix] = remove_outliers(dict["%s_mu" % prefix], outliers)
+
+ dict["nsamples"] = remove_outliers(dict["nsamples"], outliers)
diff --git a/ci/vfc_ci_report/inspect_runs.py b/ci/vfc_ci_report/inspect_runs.py
new file mode 100644
index 0000000..f53ab17
--- /dev/null
+++ b/ci/vfc_ci_report/inspect_runs.py
@@ -0,0 +1,570 @@
+# Manage the view comparing the variables of a run
+
+from math import pi
+from functools import partial
+
+import pandas as pd
+import numpy as np
+
+from bokeh.plotting import figure, curdoc
+from bokeh.embed import components
+from bokeh.models import Select, ColumnDataSource, Panel, Tabs, HoverTool,\
+ RadioButtonGroup, CheckboxGroup, CustomJS
+
+import helper
+import plot
+
+
+##########################################################################
+
+
+class InspectRuns:
+
+ # Helper functions related to InspectRun
+
+ # Returns a dictionary mapping user-readable strings to all run timestamps
+ def gen_runs_selection(self):
+
+ runs_dict = {}
+
+ # Iterate over timestamp rows (runs) and fill dict
+ for row in self.metadata.iloc:
+ # The syntax used by pandas makes this part a bit tricky :
+ # row.name is the index of metadata (so it refers to the
+ # timestamp), whereas row["name"] is the column called "name"
+ # (which is the display string used for the run)
+
+ # runs_dict[run's name] = run's timestamp
+ runs_dict[row["name"]] = row.name
+
+ return runs_dict
+
+ def gen_boxplot_tooltips(self, prefix):
+ return [
+ ("Name", "@%s_x" % prefix),
+ ("Min", "@" + prefix + "_min{%0.18e}"),
+ ("Max", "@" + prefix + "_max{%0.18e}"),
+ ("1st quartile", "@" + prefix + "_quantile25{%0.18e}"),
+ ("Median", "@" + prefix + "_quantile50{%0.18e}"),
+ ("3rd quartile", "@" + prefix + "_quantile75{%0.18e}"),
+ ("μ", "@" + prefix + "_mu{%0.18e}"),
+ ("Number of samples (tests)", "@nsamples")
+ ]
+
+ def gen_boxplot_tooltips_formatters(self, prefix):
+ return {
+ "@%s_min" % prefix: "printf",
+ "@%s_max" % prefix: "printf",
+ "@%s_quantile25" % prefix: "printf",
+ "@%s_quantile50" % prefix: "printf",
+ "@%s_quantile75" % prefix: "printf",
+ "@%s_mu" % prefix: "printf"
+ }
+
+ # Data processing helper
+ # (computes new distributions for sigma, s2, s10)
+
+ def data_processing(self, dataframe):
+
+ # Compute aggragated mu
+ dataframe["mu"] = np.vectorize(
+ np.average)(
+ dataframe["mu"],
+ weights=dataframe["nsamples"])
+
+ # nsamples is the number of aggregated elements (as well as the number
+ # of samples for our new sigma and s distributions)
+ dataframe["nsamples"] = dataframe["nsamples"].apply(lambda x: len(x))
+
+ dataframe["mu_x"] = dataframe.index
+ # Make sure that strings don't excede a certain length
+ dataframe["mu_x"] = dataframe["mu_x"].apply(
+ lambda x: x[:17] + "[...]" + x[-17:] if len(x) > 39 else x
+ )
+
+ # Get quantiles and mu for sigma, s10, s2
+ for prefix in ["sigma", "s10", "s2"]:
+
+ dataframe["%s_x" % prefix] = dataframe["mu_x"]
+
+ dataframe[prefix] = dataframe[prefix].apply(np.sort)
+
+ dataframe["%s_min" % prefix] = dataframe[prefix].apply(np.min)
+ dataframe["%s_quantile25" % prefix] = dataframe[prefix].apply(
+ np.quantile, args=(0.25,))
+ dataframe["%s_quantile50" % prefix] = dataframe[prefix].apply(
+ np.quantile, args=(0.50,))
+ dataframe["%s_quantile75" % prefix] = dataframe[prefix].apply(
+ np.quantile, args=(0.75,))
+ dataframe["%s_max" % prefix] = dataframe[prefix].apply(np.max)
+ dataframe["%s_mu" % prefix] = dataframe[prefix].apply(np.average)
+ del dataframe[prefix]
+
+ return dataframe
+
+ # Plots update function
+
+ def update_plots(self):
+
+ groupby_display = self.widgets["groupby_radio"].labels[
+ self.widgets["groupby_radio"].active
+ ]
+ groupby = self.factors_dict[groupby_display]
+
+ filterby_display = self.widgets["filterby_radio"].labels[
+ self.widgets["filterby_radio"].active
+ ]
+ filterby = self.factors_dict[filterby_display]
+
+ # Groupby and aggregate lines belonging to the same group in lists
+
+ groups = self.run_data[
+ self.run_data.index.isin(
+ [self.widgets["select_filter"].value],
+ level=filterby
+ )
+ ].groupby(groupby)
+
+ groups = groups.agg({
+ "sigma": lambda x: x.tolist(),
+ "s10": lambda x: x.tolist(),
+ "s2": lambda x: x.tolist(),
+
+ "mu": lambda x: x.tolist(),
+
+ # Used for mu weighted average first, then will be replaced
+ "nsamples": lambda x: x.tolist()
+ })
+
+ # Compute the new distributions, ...
+ groups = self.data_processing(groups).to_dict("list")
+
+ # Update source
+
+ # Assign each ColumnDataSource, starting with the boxplots
+ for prefix in ["sigma", "s10", "s2"]:
+
+ dict = {
+ "%s_x" % prefix: groups["%s_x" % prefix],
+ "%s_min" % prefix: groups["%s_min" % prefix],
+ "%s_quantile25" % prefix: groups["%s_quantile25" % prefix],
+ "%s_quantile50" % prefix: groups["%s_quantile50" % prefix],
+ "%s_quantile75" % prefix: groups["%s_quantile75" % prefix],
+ "%s_max" % prefix: groups["%s_max" % prefix],
+ "%s_mu" % prefix: groups["%s_mu" % prefix],
+
+ "nsamples": groups["nsamples"]
+ }
+
+ # Filter outliers if the box is checked
+ if len(self.widgets["outliers_filtering_inspect"].active) > 0:
+
+ # Boxplots will be filtered by max then min
+ top_outliers = helper.detect_outliers(dict["%s_max" % prefix])
+ helper.remove_boxplot_outliers(dict, top_outliers, prefix)
+
+ bottom_outliers = helper.detect_outliers(
+ dict["%s_min" % prefix])
+ helper.remove_boxplot_outliers(dict, bottom_outliers, prefix)
+
+ self.sources["%s_source" % prefix].data = dict
+
+ # Finish with the mu plot
+ dict = {
+ "mu_x": groups["mu_x"],
+ "mu": groups["mu"],
+
+ "nsamples": groups["nsamples"]
+ }
+
+ self.sources["mu_source"].data = dict
+
+ # Filter outliers if the box is checked
+ if len(self.widgets["outliers_filtering_inspect"].active) > 0:
+ mu_outliers = helper.detect_outliers(groups["mu"])
+ groups["mu"] = helper.remove_outliers(groups["mu"], mu_outliers)
+ groups["mu_x"] = helper.remove_outliers(
+ groups["mu_x"], mu_outliers)
+
+ # Update plots axis/titles
+
+ # Get display string of the last (unselected) factor
+ factors_dict = self.factors_dict.copy()
+ del factors_dict[groupby_display]
+ del factors_dict[filterby_display]
+ for_all = list(factors_dict.keys())[0]
+
+ # Update all display strings for plot title (remove caps, plural)
+ groupby_display = groupby_display.lower()
+ filterby_display = filterby_display.lower()[:-1]
+ for_all = for_all.lower()
+
+ self.plots["mu_inspect"].title.text = \
+ "Empirical average μ of %s (groupped by %s, for all %s)" \
+ % (filterby_display, groupby_display, for_all)
+
+ self.plots["sigma_inspect"].title.text = \
+ "Standard deviation σ of %s (groupped by %s, for all %s)" \
+ % (filterby_display, groupby_display, for_all)
+
+ self.plots["s10_inspect"].title.text = \
+ "Significant digits s of %s (groupped by %s, for all %s)" \
+ % (filterby_display, groupby_display, for_all)
+
+ self.plots["s2_inspect"].title.text = \
+ "Significant digits s of %s (groupped by %s, for all %s)" \
+ % (filterby_display, groupby_display, for_all)
+
+ helper.reset_x_range(self.plots["mu_inspect"], groups["mu_x"])
+ helper.reset_x_range(self.plots["sigma_inspect"], groups["sigma_x"])
+ helper.reset_x_range(self.plots["s10_inspect"], groups["s10_x"])
+ helper.reset_x_range(self.plots["s2_inspect"], groups["s2_x"])
+
+ # Widets' callback functions
+
+ # Run selector callback
+
+ def update_run(self, attrname, old, new):
+
+ filterby = self.widgets["filterby_radio"].labels[
+ self.widgets["filterby_radio"].active
+ ]
+ filterby = self.factors_dict[filterby]
+
+ # Update run selection (by using dict mapping)
+ self.current_run = self.runs_dict[new]
+
+ # Update run data
+ self.run_data = self.data[self.data["timestamp"] == self.current_run]
+
+ # Save old selected option
+ old_value = self.widgets["select_filter"].value
+
+ # Update filter options
+ options = self.run_data.index\
+ .get_level_values(filterby).drop_duplicates().tolist()
+ self.widgets["select_filter"].options = options
+
+ if old_value not in self.widgets["select_filter"].options:
+ self.widgets["select_filter"].value = options[0]
+ # The update_var callback will be triggered by the assignment
+
+ else:
+ # Trigger the callback manually (since the plots need to be updated
+ # anyway)
+ self.update_filter("", "", old_value)
+
+ # "Group by" radio
+
+ def update_groupby(self, attrname, old, new):
+
+ # Update "Filter by" radio list
+ filterby_list = list(self.factors_dict.keys())
+ del filterby_list[self.widgets["groupby_radio"].active]
+ self.widgets["filterby_radio"].labels = filterby_list
+
+ filterby = self.widgets["filterby_radio"].labels[
+ self.widgets["filterby_radio"].active
+ ]
+ filterby = self.factors_dict[filterby]
+
+ # Save old selected option
+ old_value = self.widgets["select_filter"].value
+
+ # Update filter options
+ options = self.run_data.index\
+ .get_level_values(filterby).drop_duplicates().tolist()
+ self.widgets["select_filter"].options = options
+
+ if old_value not in self.widgets["select_filter"].options:
+ self.widgets["select_filter"].value = options[0]
+ # The update_var callback will be triggered by the assignment
+
+ else:
+ # Trigger the callback manually (since the plots need to be updated
+ # anyway)
+ self.update_filter("", "", old_value)
+
+ # "Filter by" radio
+
+ def update_filterby(self, attrname, old, new):
+
+ filterby = self.widgets["filterby_radio"].labels[
+ self.widgets["filterby_radio"].active
+ ]
+ filterby = self.factors_dict[filterby]
+
+ # Save old selected option
+ old_value = self.widgets["select_filter"].value
+
+ # Update filter selector options
+ options = self.run_data.index\
+ .get_level_values(filterby).drop_duplicates().tolist()
+ self.widgets["select_filter"].options = options
+
+ if old_value not in self.widgets["select_filter"].options:
+ self.widgets["select_filter"].value = options[0]
+ # The update_var callback will be triggered by the assignment
+
+ else:
+ # Trigger the callback manually (since the plots need to be updated
+ # anyway)
+ self.update_filter("", "", old_value)
+
+ # Filter selector callback
+
+ def update_filter(self, attrname, old, new):
+ self.update_plots()
+
+ # Filter outliers checkbox callback
+
+ def update_outliers_filtering(self, attrname, old, new):
+ # The status (checked/unchecked) of the checkbox is also verified inside
+ # self.update_plots(), so calling this function is enough
+ self.update_plots()
+
+ # Bokeh setup functions
+ # (for both variable and backend selection at once)
+
+ def setup_plots(self):
+
+ tools = "pan, wheel_zoom, xwheel_zoom, ywheel_zoom, reset, save"
+
+ # Tooltips and formatters
+
+ dotplot_tooltips = [
+ ("Name", "@mu_x"),
+ ("μ", "@mu{%0.18e}"),
+ ("Number of samples (tests)", "@nsamples")
+ ]
+ dotplot_formatters = {
+ "@mu": "printf"
+ }
+
+ sigma_boxplot_tooltips = self.gen_boxplot_tooltips("sigma")
+ sigma_boxplot_tooltips_formatters = self.gen_boxplot_tooltips_formatters(
+ "sigma")
+
+ s10_boxplot_tooltips = self.gen_boxplot_tooltips("s10")
+ s10_boxplot_tooltips_formatters = self.gen_boxplot_tooltips_formatters(
+ "s10")
+
+ s2_boxplot_tooltips = self.gen_boxplot_tooltips("s2")
+ s2_boxplot_tooltips_formatters = self.gen_boxplot_tooltips_formatters(
+ "s2")
+
+ # Plots
+
+ # Mu plot
+ self.plots["mu_inspect"] = figure(
+ name="mu_inspect",
+ title="",
+ plot_width=900, plot_height=400, x_range=[""],
+ tools=tools, sizing_mode="scale_width"
+ )
+ plot.fill_dotplot(
+ self.plots["mu_inspect"], self.sources["mu_source"], "mu",
+ tooltips=dotplot_tooltips,
+ tooltips_formatters=dotplot_formatters
+ )
+ self.doc.add_root(self.plots["mu_inspect"])
+
+ # Sigma plot
+ self.plots["sigma_inspect"] = figure(
+ name="sigma_inspect",
+ title="",
+ plot_width=900, plot_height=400, x_range=[""],
+ tools=tools, sizing_mode="scale_width"
+ )
+ plot.fill_boxplot(
+ self.plots["sigma_inspect"],
+ self.sources["sigma_source"],
+ prefix="sigma",
+ tooltips=sigma_boxplot_tooltips,
+ tooltips_formatters=sigma_boxplot_tooltips_formatters)
+ self.doc.add_root(self.plots["sigma_inspect"])
+
+ # s plots
+ self.plots["s10_inspect"] = figure(
+ name="s10_inspect",
+ title="",
+ plot_width=900, plot_height=400, x_range=[""],
+ tools=tools, sizing_mode='scale_width'
+ )
+ plot.fill_boxplot(
+ self.plots["s10_inspect"],
+ self.sources["s10_source"],
+ prefix="s10",
+ tooltips=s10_boxplot_tooltips,
+ tooltips_formatters=s10_boxplot_tooltips_formatters)
+ s10_tab_inspect = Panel(
+ child=self.plots["s10_inspect"],
+ title="Base 10")
+
+ self.plots["s2_inspect"] = figure(
+ name="s2_inspect",
+ title="",
+ plot_width=900, plot_height=400, x_range=[""],
+ tools=tools, sizing_mode='scale_width'
+ )
+ plot.fill_boxplot(
+ self.plots["s2_inspect"], self.sources["s2_source"], prefix="s2",
+ tooltips=s2_boxplot_tooltips,
+ tooltips_formatters=s2_boxplot_tooltips_formatters
+ )
+ s2_tab_inspect = Panel(child=self.plots["s2_inspect"], title="Base 2")
+
+ s_tabs_inspect = Tabs(
+ name="s_tabs_inspect",
+ tabs=[s10_tab_inspect, s2_tab_inspect], tabs_location="below"
+ )
+ self.doc.add_root(s_tabs_inspect)
+
+ def setup_widgets(self):
+
+ # Generation of selectable items
+
+ # Dict contains all inspectable runs (maps display strings to timestamps)
+ # The dict structure allows to get the timestamp from the display string
+ # in O(1)
+ self.runs_dict = self.gen_runs_selection()
+
+ # Dict maps display strings to column names for the different factors
+ # (var, backend, test)
+ self.factors_dict = {
+ "Variables": "variable",
+ "Backends": "vfc_backend",
+ "Tests": "test"
+ }
+
+ # Run selection
+
+ # Contains all options strings
+ runs_display = list(self.runs_dict.keys())
+ # Will be used when updating plots (contains actual number)
+ self.current_run = self.runs_dict[runs_display[-1]]
+ # Contains the selected option string, used to update current_n_runs
+ current_run_display = runs_display[-1]
+ # This contains only entries matching the run
+ self.run_data = self.data[self.data["timestamp"] == self.current_run]
+
+ change_run_callback_js = "updateRunMetadata(cb_obj.value);"
+
+ self.widgets["select_run"] = Select(
+ name="select_run", title="Run :",
+ value=current_run_display, options=runs_display
+ )
+ self.doc.add_root(self.widgets["select_run"])
+ self.widgets["select_run"].on_change("value", self.update_run)
+ self.widgets["select_run"].js_on_change("value", CustomJS(
+ code=change_run_callback_js,
+ args=(dict(
+ metadata=helper.metadata_to_dict(
+ helper.get_metadata(self.metadata, self.current_run)
+ )
+ ))
+ ))
+
+ # Factors selection
+
+ # "Group by" radio
+ self.widgets["groupby_radio"] = RadioButtonGroup(
+ name="groupby_radio",
+ labels=list(self.factors_dict.keys()), active=0
+ )
+ self.doc.add_root(self.widgets["groupby_radio"])
+ # The functions are defined inside the template to avoid writing too
+ # much JS server side
+ self.widgets["groupby_radio"].on_change(
+ "active",
+ self.update_groupby
+ )
+
+ # "Filter by" radio
+ # Get all possible factors, and remove the one selected in "Group by"
+ filterby_list = list(self.factors_dict.keys())
+ del filterby_list[self.widgets["groupby_radio"].active]
+
+ self.widgets["filterby_radio"] = RadioButtonGroup(
+ name="filterby_radio",
+ labels=filterby_list, active=0
+ )
+ self.doc.add_root(self.widgets["filterby_radio"])
+ # The functions are defined inside the template to avoid writing too
+ # much JS server side
+ self.widgets["filterby_radio"].on_change(
+ "active",
+ self.update_filterby
+ )
+
+ # Filter selector
+
+ filterby = self.widgets["filterby_radio"].labels[
+ self.widgets["filterby_radio"].active
+ ]
+ filterby = self.factors_dict[filterby]
+
+ options = self.run_data.index\
+ .get_level_values(filterby).drop_duplicates().tolist()
+
+ self.widgets["select_filter"] = Select(
+ # We need a different name to avoid collision in the template with
+ # the runs comparison's widget
+ name="select_filter", title="Select a filter :",
+ value=options[0], options=options
+ )
+ self.doc.add_root(self.widgets["select_filter"])
+ self.widgets["select_filter"]\
+ .on_change("value", self.update_filter)
+
+ # Toggle for outliers filtering
+
+ self.widgets["outliers_filtering_inspect"] = CheckboxGroup(
+ name="outliers_filtering_inspect",
+ labels=["Filter outliers"], active=[]
+ )
+ self.doc.add_root(self.widgets["outliers_filtering_inspect"])
+ self.widgets["outliers_filtering_inspect"]\
+ .on_change("active", self.update_outliers_filtering)
+
+ # Communication methods
+ # (to send/receive messages to/from master)
+
+ # When received, switch to the run_name in parameter
+
+ def switch_view(self, run_name):
+ self.widgets["select_run"].value = run_name
+
+ # Constructor
+
+ def __init__(self, master, doc, data, metadata):
+
+ self.master = master
+
+ self.doc = doc
+ self.data = data
+ self.metadata = metadata
+
+ self.sources = {
+ "mu_source": ColumnDataSource(data={}),
+ "sigma_source": ColumnDataSource(data={}),
+ "s10_source": ColumnDataSource(data={}),
+ "s2_source": ColumnDataSource(data={})
+ }
+
+ self.plots = {}
+ self.widgets = {}
+
+ # Setup Bokeh objects
+ self.setup_plots()
+ self.setup_widgets()
+
+ # Pass the initial metadata to the template (will be updated in CustomJS
+ # callbacks). This is required because metadata is not displayed in a
+ # Bokeh widget, so we can't update this with a server callback.
+ initial_run = helper.get_metadata(self.metadata, self.current_run)
+ self.doc.template_variables["initial_timestamp"] = self.current_run
+
+ # At this point, everything should have been initialized, so we can
+ # show the plots for the first time
+ self.update_plots()
diff --git a/ci/vfc_ci_report/main.py b/ci/vfc_ci_report/main.py
new file mode 100644
index 0000000..4af73d2
--- /dev/null
+++ b/ci/vfc_ci_report/main.py
@@ -0,0 +1,208 @@
+# Look for and read all the run files in the current directory (ending with
+# .vfcrunh5), and lanch a Bokeh server for the visualization of this data.
+
+import os
+import sys
+import time
+
+import pandas as pd
+
+from bokeh.plotting import curdoc
+
+# Local imports from vfc_ci_server
+import compare_runs
+import inspect_runs
+import helper
+
+##########################################################################
+
+# Read vfcrun files, and aggregate them in one dataset
+
+run_files = [f for f in os.listdir(".") if f.endswith(".vfcrun.h5")]
+
+if len(run_files) == 0:
+ print(
+ "Warning [vfc_ci]: Could not find any vfcrun files in the directory. "
+ "This will result in server errors and prevent you from viewing the report.")
+
+# These are arrays of Pandas dataframes for now
+metadata = []
+data = []
+
+for f in run_files:
+ metadata.append(pd.read_hdf(f, "metadata"))
+ data.append(pd.read_hdf(f, "data"))
+
+metadata = pd.concat(metadata).sort_index()
+data = pd.concat(data).sort_index()
+
+
+# Generate the display strings for runs (runs ticks)
+# By doing this in master, we ensure the homogeneity of display strings
+# across all plots
+metadata["name"] = metadata.index.to_series().map(
+ lambda x: helper.get_run_name(
+ x,
+ helper.get_metadata(metadata, x)["hash"]
+ )
+)
+helper.reset_run_strings()
+
+metadata["date"] = metadata.index.to_series().map(
+ lambda x: time.ctime(x)
+)
+
+
+##########################################################################
+
+
+curdoc().title = "Verificarlo Report"
+
+# Read server arguments
+# (this is quite easy because Bokeh server is called through a wrapper, so
+# we know exactly what the arguments might be)
+
+git_repo_linked = False
+commit_link = ""
+
+has_logo = False
+logo_url = ""
+
+for i in range(1, len(sys.argv)):
+
+ # Look for the Git repository remote address
+ # (if a Git repo is specified, the webpage will contain hyperlinks to the
+ # repository and the different commits)
+ if sys.argv[i] == "git":
+ from urllib.parse import urlparse
+
+ method = sys.argv[i + 1]
+ address = sys.argv[i + 2]
+ url = ""
+
+ # Here, address is either the remote URL or the path to the local Git
+ # repo (depending on the method)
+
+ if method == "url":
+ # We should directly have a Git URL
+ url = address
+
+ elif method == "directory":
+ # Get the remote URL from the local repo
+ from git import Repo
+ repo = Repo(address)
+ url = repo.remotes.origin.url
+
+ else:
+ raise ValueError(
+ "Error [vfc_ci]: The specified method to get the Git "
+ "repository is invalid. Are you calling Bokeh directly "
+ "instead of using the Verificarlo wrapper ?"
+ )
+
+ # At this point, "url" should be set correctly, we can get the repo's
+ # URL and name, after making sure we're on a Git URL
+
+ parsed_url = urlparse(url)
+
+ path = parsed_url.path.split("/")
+ if len(path) < 3:
+ raise ValueError(
+ "Error [vfc_ci]: The found URL doesn't seem to be pointing "
+ "to a Git repository (path is too short)"
+ )
+
+ repo_name = path[2]
+
+ curdoc().template_variables["repo_url"] = url
+ curdoc().template_variables["repo_name"] = repo_name
+
+ # We should have a "github.com" or a "*gitlab*" URL
+
+ if parsed_url.netloc == "github.com":
+ commit_link = "https://%s%s/commit/" \
+ % (parsed_url.netloc, parsed_url.path)
+
+ curdoc().template_variables["commit_link"] = commit_link
+ curdoc().template_variables["git_host"] = "GitHub"
+
+ # Used in Bokeh tooltips
+ commit_link = commit_link + "@hash"
+
+ # We assume we have a GitLab URL
+ else:
+ commit_link = "https://%s%s/-/commit/" \
+ % (parsed_url.netloc, parsed_url.path)
+
+ curdoc().template_variables["commit_link"] = commit_link
+ curdoc().template_variables["git_host"] = "GitLab"
+
+ # Used in Bokeh tooltips
+ commit_link = commit_link + "@hash"
+
+ git_repo_linked = True
+
+ # Look for a logo URL
+ # If a logo URL is specified, it will be included in the report's header
+ if sys.argv[i] == "logo":
+ curdoc().template_variables["logo_url"] = sys.argv[i + 1]
+ has_logo = True
+
+
+# After the loop, we know if a repo has been linked, if we have a logo, ...
+curdoc().template_variables["git_repo_linked"] = git_repo_linked
+curdoc().template_variables["has_logo"] = has_logo
+
+
+##########################################################################
+
+# Setup report views
+
+# Define a ViewsMaster class to allow two-ways communication between views.
+# This approach by classes allows us to have separate scopes for each view and
+# will be useful if we want to add new views at some point in the future
+# (instead of having n views with n-1 references each).
+
+class ViewsMaster:
+
+ # Communication functions
+
+ def go_to_inspect(self, run_name):
+ self.inspect.switch_view(run_name)
+
+ # Constructor
+
+ def __init__(self, data, metadata, git_repo_linked, commit_link):
+
+ self.data = data
+ self.metadata = metadata
+ self.git_repo_linked = git_repo_linked
+ self.commit_link = commit_link
+
+ # Pass metadata to the template as a JSON string
+ curdoc().template_variables["metadata"] = self.metadata.to_json(
+ orient="index")
+
+ # Runs comparison
+ self.compare = compare_runs.CompareRuns(
+ master=self,
+ doc=curdoc(),
+ data=data,
+ metadata=metadata,
+ )
+
+ # Runs inspection
+ self.inspect = inspect_runs.InspectRuns(
+ master=self,
+ doc=curdoc(),
+ data=data,
+ metadata=metadata,
+ )
+
+
+views_master = ViewsMaster(
+ data=data,
+ metadata=metadata,
+ git_repo_linked=git_repo_linked,
+ commit_link=commit_link
+)
diff --git a/ci/vfc_ci_report/plot.py b/ci/vfc_ci_report/plot.py
new file mode 100644
index 0000000..f4bb20f
--- /dev/null
+++ b/ci/vfc_ci_report/plot.py
@@ -0,0 +1,142 @@
+# General functions for filling plots with data in all report's views
+
+from bokeh.plotting import figure
+from bokeh.models import HoverTool, TapTool, CustomJS
+
+from math import pi
+
+
+def fill_dotplot(
+ plot, source, data_field,
+ tooltips=None, tooltips_formatters=None,
+ js_tap_callback=None, server_tap_callback=None,
+ lines=False,
+ lower_bound=False
+):
+
+ # (Optional) Tooltip and tooltip formatters
+ if tooltips is not None:
+ hover = HoverTool(tooltips=tooltips, mode="vline", names=["circle"])
+
+ if tooltips_formatters is not None:
+ hover.formatters = tooltips_formatters
+
+ plot.add_tools(hover)
+
+ # (Optional) Add TapTool (for JS tap callback)
+ if js_tap_callback is not None:
+ tap = TapTool(callback=CustomJS(code=js_tap_callback))
+ plot.add_tools(tap)
+
+ # (Optional) Add segment to represent a lower bound
+ if lower_bound:
+ lower_segment = plot.segment(
+ x0="%s_x" % data_field, y0=data_field,
+ x1="%s_x" % data_field, y1="%s_lower_bound" % data_field,
+ source=source, line_color="black"
+ )
+
+ # Draw dots (actually Bokeh circles)
+ circle = plot.circle(
+ name="circle",
+ x="%s_x" % data_field, y=data_field, source=source, size=12
+ )
+
+ # (Optional) Draw lines between dots
+ if lines:
+ line = plot.line(x="%s_x" % data_field, y=data_field, source=source)
+
+ # (Optional) Add server tap callback
+ if server_tap_callback is not None:
+ circle.data_source.selected.on_change("indices", server_tap_callback)
+
+ # Plot appearance
+ plot.xgrid.grid_line_color = None
+ plot.ygrid.grid_line_color = None
+
+ plot.yaxis[0].formatter.power_limit_high = 0
+ plot.yaxis[0].formatter.power_limit_low = 0
+ plot.yaxis[0].formatter.precision = 3
+
+ plot.xaxis[0].major_label_orientation = pi / 8
+
+
+def fill_boxplot(
+ plot, source,
+ prefix="",
+ tooltips=None, tooltips_formatters=None,
+ js_tap_callback=None, server_tap_callback=None
+):
+
+ # (Optional) Tooltip and tooltip formatters
+ if tooltips is not None:
+ hover = HoverTool(tooltips=tooltips, mode="vline", names=["full_box"])
+
+ if tooltips_formatters is not None:
+ hover.formatters = tooltips_formatters
+
+ plot.add_tools(hover)
+
+ # (Optional) Add TapTool (for JS tap callback)
+ if js_tap_callback is not None:
+ tap = TapTool(callback=CustomJS(code=js_tap_callback))
+ plot.add_tools(tap)
+
+ # Draw boxes (the prefix argument modifies the fields of ColumnDataSource
+ # that are used)
+
+ if prefix != "":
+ prefix = "%s_" % prefix
+
+ # Stems
+ top_stem = plot.segment(
+ x0="%sx" % prefix, y0="%smax" % prefix,
+ x1="%sx" % prefix, y1="%squantile75" % prefix,
+ source=source, line_color="black"
+ )
+ bottom_stem = plot.segment(
+ x0="%sx" % prefix, y0="%smin" % prefix,
+ x1="%sx" % prefix, y1="%squantile25" % prefix,
+ source=source, line_color="black"
+ )
+
+ # Boxes
+ full_box = plot.vbar(
+ name="full_box",
+ x="%sx" % prefix, width=0.5,
+ top="%squantile75" % prefix, bottom="%squantile25" % prefix,
+ source=source, line_color="black"
+ )
+ bottom_box = plot.vbar(
+ x="%sx" % prefix, width=0.5,
+ top="%squantile50" % prefix, bottom="%squantile25" % prefix,
+ source=source, line_color="black"
+ )
+
+ # Mu dot
+ mu_dot = plot.dot(
+ x="%sx" % prefix, y="%smu" % prefix, size=30, source=source,
+ color="black"
+ )
+
+ # (Optional) Add server tap callback
+ if server_tap_callback is not None:
+ top_stem.data_source.selected.on_change("indices", server_tap_callback)
+ bottom_stem.data_source.selected.on_change(
+ "indices", server_tap_callback)
+
+ full_box.data_source.selected.on_change("indices", server_tap_callback)
+ bottom_box.data_source.selected.on_change(
+ "indices", server_tap_callback)
+
+ mu_dot.data_source.selected.on_change("indices", server_tap_callback)
+
+ # Plot appearance
+ plot.xgrid.grid_line_color = None
+ plot.ygrid.grid_line_color = None
+
+ plot.yaxis[0].formatter.power_limit_high = 0
+ plot.yaxis[0].formatter.power_limit_low = 0
+ plot.yaxis[0].formatter.precision = 3
+
+ plot.xaxis[0].major_label_orientation = pi / 8
diff --git a/ci/vfc_ci_report/templates/index.html b/ci/vfc_ci_report/templates/index.html
new file mode 100644
index 0000000..8fea8ec
--- /dev/null
+++ b/ci/vfc_ci_report/templates/index.html
@@ -0,0 +1,482 @@
+
+
+
+
+ Verificarlo Report
+
+
+
+
+
+
+
+
+
+ {% extends base %}
+
+
+
+
+ {% block contents %}
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
Selectors
+
+ {{ embed(roots.test_filter) }}
+ {{ embed(roots.select_test) }}
+
+ {{ embed(roots.select_var) }}
+
+ {{ embed(roots.select_backend) }}
+
+ {{ embed(roots.outliers_filtering_compare) }}
+
+
+ {{ embed(roots.select_n_runs) }}
+
+
+
+
+
+ Tip : You can click on any element of the plots
+ to inspect the corresponding run in details.
+
+
+
+
+
+
+
+
+
Plots
+
+
+ {{ embed(roots.s_tabs) }}
+
+
+
+
+
+ {{ embed(roots.sigma_plot) }}
+
+
+
+
+
+ {{ embed(roots.boxplot) }}
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
Selectors
+ {{ embed(roots.select_run) }}
+
+
+
+ Group by :
+ {{ embed(roots.groupby_radio) }}
+
+
+
+ Filter by :
+ {{ embed(roots.filterby_radio) }}
+ {{ embed(roots.select_filter) }}
+
+
+
+ {{ embed(roots.outliers_filtering_inspect) }}
+
+
+
+
+
Run metadata
+
+
Date :
+
+
+
+
+
+
+
+
+
+ This run is not linked to a Git commit.
+
+
+
+
+
+
+
+
+
Plots
+
+ {{ embed(roots.s_tabs_inspect) }}
+
+
+
+
+
+ {{ embed(roots.sigma_inspect) }}
+
+
+
+
+
+ {{ embed(roots.mu_inspect) }}
+
+
+
+
+
+
+
+
+
+
+
+
+ {% if has_logo %}
+
+ {% else %}
+
+ {% endif %}
+
+
+
+
+
+
+
+ {% endblock %}
+
+
+
diff --git a/ci/workflow_templates/ci_README.j2.md b/ci/workflow_templates/ci_README.j2.md
new file mode 100644
index 0000000..a41ca96
--- /dev/null
+++ b/ci/workflow_templates/ci_README.j2.md
@@ -0,0 +1,7 @@
+## Verificarlo CI : `{{dev_branch}}`
+
+You are on the `{{ci_branch}}` branch, which is automatically updated with the
+[Verificarlo](https://github.com/verificarlo/verificarlo) test results from
+`{{dev_branch}}` (in the `vfcruns` directory).
+
+You can start a Verificarlo CI server at anytime using the run files of this branch.
diff --git a/ci/workflow_templates/gitlab-ci.j2.yml b/ci/workflow_templates/gitlab-ci.j2.yml
new file mode 100644
index 0000000..de26aeb
--- /dev/null
+++ b/ci/workflow_templates/gitlab-ci.j2.yml
@@ -0,0 +1,42 @@
+# This workflow will be executed when {{dev_branch}} is updated:
+# it will run the configured tests and upload the results on vfc_ci_master.
+
+image: verificarlo/verificarlo
+
+
+stages:
+ - run_verificarlo_tests
+
+
+run_verificarlo_tests:
+ stage: run_verificarlo_tests
+
+ before_script:
+ - git remote set-url origin https://{{username}}:${CI_PUSH_TOKEN}@{{remote_url}}.git
+ - git config --global user.email "{{email}}"
+ - git config --global user.name "{{username}}"
+
+ script:
+ # We will probably drop these installations when integrating CI into
+ # Verificarlo
+ - pip install numpy scipy pandas bokeh jinja2 tables GitPython
+ - apt update
+ - apt install wget
+ - wget https://raw.githubusercontent.com/verificarlo/significantdigits/main/sigdigits.py -P /usr/local/lib/python3.8/dist-packages
+
+ - ./vfc_ci test -g -r
+ - git_hash=$(git rev-parse --short "$CI_COMMIT_SHA")
+ - git fetch --all
+ - git checkout -b {{ci_branch}} origin/{{ci_branch}}
+ - mkdir -p vfcruns
+ - mv *.vfcrun.h5 vfcruns
+ - git add vfcruns/*
+ - git commit -m "[auto] New test results for commit ${git_hash}"
+ - git push
+
+ rules:
+ - if: '$CI_COMMIT_BRANCH == "{{dev_branch}}"'
+
+ artifacts:
+ paths:
+ - "*.vfcraw.h5"
diff --git a/ci/workflow_templates/vfc_test_workflow.j2.yml b/ci/workflow_templates/vfc_test_workflow.j2.yml
new file mode 100644
index 0000000..b39e21e
--- /dev/null
+++ b/ci/workflow_templates/vfc_test_workflow.j2.yml
@@ -0,0 +1,57 @@
+# This workflow will be executed when {{dev_branch}} is updated:
+# it will run the configured tests and upload the results on {{ci_branch}}.
+
+name: "Verificarlo CI ({{dev_branch}})"
+
+on:
+ # Triggers the workflow when {{dev_branch}} is updated
+ push:
+ branches: [ {{dev_branch}} ]
+
+ workflow_dispatch:
+
+
+jobs:
+ run_verificarlo_tests:
+ runs-on: ubuntu-latest
+ container: verificarlo/verificarlo
+
+ steps:
+ - uses: actions/checkout@v2
+ with:
+ fetch-depth: 0
+
+ # We will probably drop these installations when integrating CI into
+ # Verificarlo
+ - name: Install Python requirements
+ run: |
+ pip install numpy scipy pandas bokeh jinja2 tables GitPython
+ apt update
+ apt install wget
+ wget https://raw.githubusercontent.com/verificarlo/significantdigits/main/sigdigits.py -P /usr/local/lib/python3.8/dist-packages
+
+ - name: Run tests
+ # We assume the script is included in the repo for now
+ # (we'll probably want to remove "./" if the script ends up being integrated
+ # in Verificarlo and becomes available system-wide)
+ run: ./vfc_ci test -g -r
+
+ - name: Commit test results
+ run: |
+ git_hash=$(git rev-parse --short "$GITHUB_SHA")
+
+ git config --local user.email "action@github.com"
+ git config --local user.name "GitHub Action"
+
+ git checkout {{ci_branch}}
+ mkdir -p vfcruns
+ mv *.vfcrun.h5 vfcruns
+ git add vfcruns/*
+ git commit -m "[auto] New test results for commit ${git_hash}"
+ git push
+
+ - name: Upload raw results as artifacts
+ uses: actions/upload-artifact@v2
+ with:
+ {% raw %}name: ${{github.sha}}.vfcraw{% endraw %}
+ path: ./*.vfcraw.h5
diff --git a/datasets/ci_dataset.hdf5 b/datasets/ci_dataset.hdf5
new file mode 100644
index 0000000..c7c91c2
Binary files /dev/null and b/datasets/ci_dataset.hdf5 differ
diff --git a/include/vfc_hashmap.h b/include/vfc_hashmap.h
new file mode 100644
index 0000000..c314f0e
--- /dev/null
+++ b/include/vfc_hashmap.h
@@ -0,0 +1,248 @@
+/* -*- Mode: C; tab-width: 4; c-basic-offset: 4; indent-tabs-mode: nil -*- */
+/*
+ * Copyright 2012 Couchbase, Inc.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+#include
+
+#define HASH_MULTIPLIER 31
+static const unsigned int hashmap_prime_1 = 73;
+static const unsigned int hashmap_prime_2 = 5009;
+
+#ifndef __VFC_HASHMAP_HEADER__
+
+struct vfc_hashmap_st {
+ size_t nbits;
+ size_t mask;
+
+ size_t capacity;
+ size_t *items;
+ size_t nitems;
+ size_t n_deleted_items;
+};
+typedef struct vfc_hashmap_st *vfc_hashmap_t;
+
+// allocate and initialize the map
+vfc_hashmap_t vfc_hashmap_create();
+
+// get the value at an index of a map
+size_t get_value_at(size_t *items, size_t i);
+
+// get the key at an index of a map
+size_t get_key_at(size_t *items, size_t i);
+
+// set the value at an index of a map
+void set_value_at(size_t *items, size_t value, size_t i);
+
+// set the key at an index of a map
+void set_key_at(size_t *items, size_t key, size_t i);
+
+// free the map
+void vfc_hashmap_destroy(vfc_hashmap_t map);
+
+// insert an element in the map
+void vfc_hashmap_insert(vfc_hashmap_t map, size_t key, void *item);
+
+// remove an element of the map
+void vfc_hashmap_remove(vfc_hashmap_t map, size_t key);
+
+// test if an element is in the map
+char vfc_hashmap_have(vfc_hashmap_t map, size_t key);
+
+// get an element of the map
+void *vfc_hashmap_get(vfc_hashmap_t map, size_t key);
+
+// get the number of elements in the map
+size_t vfc_hashmap_num_items(vfc_hashmap_t map);
+
+// Hash function
+size_t vfc_hashmap_str_function(const char *id);
+
+#endif
+
+/***************** Verificarlo hashmap FUNCTIONS ********************
+ * The following set of functions are used in backends and wrapper
+ * to stock and access quickly internal data.
+ *******************************************************************/
+
+// free the map
+void vfc_hashmap_destroy(vfc_hashmap_t map) {
+ if (map) {
+ free(map->items);
+ }
+ free(map);
+}
+
+// allocate and initialize the map
+vfc_hashmap_t vfc_hashmap_create() {
+ vfc_hashmap_t map = (vfc_hashmap_t) calloc(1, sizeof(struct vfc_hashmap_st));
+
+ if (map == NULL) {
+ return NULL;
+ }
+ map->nbits = 3;
+ map->capacity = (size_t)(1 << map->nbits);
+ map->mask = map->capacity - 1;
+ // an item is now a value and a key
+ map->items = (size_t *) calloc(map->capacity, 2 * sizeof(size_t));
+ if (map->items == NULL) {
+ vfc_hashmap_destroy(map);
+ return NULL;
+ }
+ map->nitems = 0;
+ map->n_deleted_items = 0;
+ return map;
+}
+
+size_t get_value_at(size_t *items, size_t i) { return items[i * 2]; }
+
+size_t get_key_at(size_t *items, size_t i) { return items[(i * 2) + 1]; }
+
+void set_value_at(size_t *items, size_t value, size_t i) {
+ items[i * 2] = value;
+}
+
+void set_key_at(size_t *items, size_t key, size_t i) {
+ items[(i * 2) + 1] = key;
+}
+
+// add a member in the table
+static int hashmap_add_member(vfc_hashmap_t map, size_t key, void *item) {
+ size_t value = (size_t)item;
+ size_t ii;
+
+ if (value == 0 || value == 1) {
+ return -1;
+ }
+
+ ii = map->mask & (hashmap_prime_1 * key);
+
+ while (get_value_at(map->items, ii) != 0 &&
+ get_value_at(map->items, ii) != 1) {
+ if (get_value_at(map->items, ii) == value) {
+ return 0;
+ } else {
+ /* search free slot */
+ ii = map->mask & (ii + hashmap_prime_2);
+ }
+ }
+ map->nitems++;
+ if (get_value_at(map->items, ii) == 1) {
+ map->n_deleted_items--;
+ }
+
+ set_value_at(map->items, value, ii);
+ set_key_at(map->items, key, ii);
+
+ return 1;
+}
+
+// rehash the table if necessary
+static void maybe_rehash_map(vfc_hashmap_t map) {
+ size_t *old_items;
+ size_t old_capacity, ii;
+
+ if (map->nitems + map->n_deleted_items >= (double)map->capacity * 0.85) {
+ old_items = map->items;
+ old_capacity = map->capacity;
+ map->nbits++;
+ map->capacity = (size_t)(1 << map->nbits);
+ map->mask = map->capacity - 1;
+ map->items = (size_t *) calloc(map->capacity, 2 * sizeof(size_t));
+ map->nitems = 0;
+ map->n_deleted_items = 0;
+ for (ii = 0; ii < old_capacity; ii++) {
+ hashmap_add_member(map, get_key_at(old_items, ii),
+ (void *)get_value_at(old_items, ii));
+ }
+ free(old_items);
+ }
+}
+
+// insert an element in the map
+void vfc_hashmap_insert(vfc_hashmap_t map, size_t key, void *item) {
+ hashmap_add_member(map, key, item);
+ maybe_rehash_map(map);
+}
+
+// remove an element of the map
+void vfc_hashmap_remove(vfc_hashmap_t map, size_t key) {
+ size_t ii = map->mask & (hashmap_prime_1 * key);
+
+ while (get_value_at(map->items, ii) != 0) {
+ if (get_key_at(map->items, ii) == key) {
+ set_value_at(map->items, 1, ii);
+ map->nitems--;
+ map->n_deleted_items++;
+ break;
+ } else {
+ ii = map->mask & (ii + hashmap_prime_2);
+ }
+ }
+}
+
+// test if an element is in the map
+char vfc_hashmap_have(vfc_hashmap_t map, size_t key) {
+ size_t ii = map->mask & (hashmap_prime_1 * key);
+
+ while (get_value_at(map->items, ii) != 0) {
+ if (get_key_at(map->items, ii) == key) {
+ return 1;
+ } else {
+ ii = map->mask & (ii + hashmap_prime_2);
+ }
+ }
+ return 0;
+}
+
+// get an element of the map
+void *vfc_hashmap_get(vfc_hashmap_t map, size_t key) {
+ size_t ii = map->mask & (hashmap_prime_1 * key);
+
+ while (get_value_at(map->items, ii) != 0) {
+ if (get_key_at(map->items, ii) == key) {
+ return (void *)get_value_at(map->items, ii);
+ } else {
+ ii = map->mask & (ii + hashmap_prime_2);
+ }
+ }
+ return NULL;
+}
+
+// get the number of elements in the map
+size_t vfc_hashmap_num_items(vfc_hashmap_t map) { return map->nitems; }
+
+// Hash function for strings
+size_t vfc_hashmap_str_function(const char *id) {
+ unsigned const char *us;
+
+ us = (unsigned const char *)id;
+
+ size_t index = 0;
+
+ while (*us != '\0') {
+ index = index * HASH_MULTIPLIER + *us;
+ us++;
+ }
+
+ return index;
+}
+
+// Free the hashmap
+void vfc_hashmap_free(vfc_hashmap_t map) {
+ for (int ii = 0; ii < map->capacity; ii++)
+ if (get_value_at(map->items, ii) != 0 && get_value_at(map->items, ii) != 0)
+ free((void *)get_value_at(map->items, ii));
+}
diff --git a/include/vfc_probe.h b/include/vfc_probe.h
new file mode 100644
index 0000000..0d716d1
--- /dev/null
+++ b/include/vfc_probe.h
@@ -0,0 +1,254 @@
+/*
+* This file defines "vfc_probes", a hashtable-based structure which can be used
+* to place "probes" in a code and store the different values of test variables.
+* These test results can then be exported in a CSV file, and used to generate a
+* Verificarlo test report.
+*/
+
+
+#include
+#include
+#include
+
+#include "vfc_hashmap.h"
+
+#define VAR_NAME(var) #var // Simply returns the name of var into a string
+
+
+/*
+* A probe containing a double value as well as its key, which is needed when
+* dumping the probes
+*/
+
+struct vfc_probe_node {
+ char * key;
+ double value;
+};
+
+typedef struct vfc_probe_node vfc_probe_node;
+
+
+
+/*
+* The probes structure. It simply acts as a wrapper for a Verificarlo hashmap.
+*/
+
+struct vfc_probes {
+ vfc_hashmap_t map;
+};
+
+typedef struct vfc_probes vfc_probes;
+
+
+/*
+* Initialize an empty vfc_probes instance
+*/
+
+vfc_probes vfc_init_probes() {
+ vfc_probes probes;
+ probes.map = vfc_hashmap_create();
+
+ return probes;
+}
+
+
+
+/*
+* Free all probes
+*/
+
+void vfc_free_probes(vfc_probes * probes) {
+
+ // Before freeing the map, iterate manually over all items to free the keys
+ vfc_probe_node * probe = NULL;
+ for(int i = 0; i < probes->map->capacity; i++) {
+ probe = (vfc_probe_node*) get_value_at(probes->map->items, i);
+ if(probe != NULL) {
+ if(probe->key != NULL) {
+ free(probe->key);
+ }
+ }
+ }
+
+ vfc_hashmap_free(probes->map);
+}
+
+
+
+/*
+* Helper function to generate the key from test and variable name
+*/
+
+char * gen_probe_key(char * testName, char * varName) {
+ char * key = (char *) malloc(strlen(testName) + strlen(varName) + 2);
+ strcpy(key, testName);
+ strcat(key, ",");
+ strcat(key, varName);
+
+ return key;
+}
+
+
+
+/*
+* Helper function to detect forbidden character ',' in the keys
+*/
+
+void validate_probe_key(char * str) {
+ unsigned int len = strlen(str);
+
+ for(unsigned int i=0; imap, vfc_hashmap_str_function(key)
+ );
+
+ if(oldProbe != NULL) {
+ if(strcmp(key, oldProbe->key) == 0) {
+ fprintf(
+ stderr,
+ "Error [verificarlo]: you have a duplicate error with one of \
+ your probes (\"%s\"). Please make sure to use different names.\n",
+ key
+ );
+ exit(1);
+ }
+ }
+
+ // Insert the element in the hashmap
+ vfc_probe_node * newProbe = (vfc_probe_node*) malloc(sizeof(vfc_probe_node));
+ newProbe->key = key;
+ newProbe->value = val;
+
+ vfc_hashmap_insert(
+ probes->map, vfc_hashmap_str_function(key), newProbe
+ );
+
+ return 0;
+}
+
+
+
+/*
+* Remove (free) an element from the hash table
+*/
+
+int vfc_remove_probe(vfc_probes * probes, char * testName, char * varName) {
+
+ if(probes == NULL) {
+ return 1;
+ }
+
+ // Get the key, which is : testName + "," + varName
+ char * key = gen_probe_key(testName, varName);
+
+ vfc_hashmap_remove(probes->map, vfc_hashmap_str_function(key));
+
+ return 0;
+}
+
+
+
+/*
+* Return the number of probes stored in the hashmap
+*/
+
+unsigned int vfc_num_probes(vfc_probes * probes) {
+ return vfc_hashmap_num_items(probes->map);
+}
+
+
+
+/*
+* Dump probes in a .csv file (the double values are converted to hex), then
+* free it.
+*/
+
+int vfc_dump_probes(vfc_probes * probes) {
+
+ if(probes == NULL) {
+ return 1;
+ }
+
+ // Get export path from the VFC_PROBES_OUTPUT env variable
+ char* exportPath = getenv("VFC_PROBES_OUTPUT");
+ if(!exportPath) {
+ printf(
+ "Warning [verificarlo]: VFC_PROBES_OUTPUT is not set, probes will \
+ not be dumped\n"
+ );
+ vfc_free_probes(probes);
+ return 0;
+ }
+
+ FILE * fp = fopen(exportPath, "w");
+
+ if(fp == NULL) {
+ fprintf(
+ stderr,
+ "Error [verificarlo]: impossible to open the CSV file to save your \
+ probes (\"%s\")\n",
+ exportPath
+ );
+ exit(1);
+ }
+
+ // First line gives the column names
+ fprintf(fp, "test,variable,value\n");
+
+ // Iterate over all table elements
+ vfc_probe_node * probe = NULL;
+ for(int i = 0; i < probes->map->capacity; i++) {
+ probe = (vfc_probe_node*) get_value_at(probes->map->items, i);
+ if(probe != NULL) {
+ fprintf(
+ fp, "%s,%a\n",
+ probe->key,
+ probe->value
+ );
+ }
+ }
+
+ fclose(fp);
+
+ vfc_free_probes(probes);
+
+ return 0;
+}
diff --git a/tests/vfc_test_h5.cpp b/tests/vfc_test_h5.cpp
new file mode 100644
index 0000000..52b2bb6
--- /dev/null
+++ b/tests/vfc_test_h5.cpp
@@ -0,0 +1,202 @@
+// This files is almost the same as test_h5.cpp, with the difference that it
+// dumps Verificarlo probes for vfc_ci integration, and that it reads a list of
+// cycles in a CSV file, instead of accepting a start and an end cycle (which
+// makes it easier to select the exact cycles we are interested in with vfc_ci).
+
+#include
+#include
+
+#include
+#include
+#include
+
+
+#include "SM_MaponiA3.hpp"
+#include "SM_Standard.hpp"
+#include "SM_Helpers.hpp"
+#include "vfc_probe.h"
+
+using namespace H5;
+// #define DEBUG
+
+const H5std_string FILE_NAME( "datasets/ci_dataset.hdf5" );
+
+double residual_max(double * A, unsigned int Dim) {
+ double max = 0.0;
+ for (unsigned int i = 0; i < Dim; i++) {
+ for (unsigned int j = 0; j < Dim; j++) {
+ double delta = (A[i * Dim + j] - (i == j));
+ delta = abs(delta);
+ if (delta > max) max = delta;
+ }
+ }
+ return max;
+}
+
+double residual2(double * A, unsigned int Dim) {
+ double res = 0.0;
+ for (unsigned int i = 0; i < Dim; i++) {
+ for (unsigned int j = 0; j < Dim; j++) {
+ double delta = (A[i * Dim + j] - (i == j));
+ res += delta*delta;
+ }
+ }
+ return res;
+}
+
+void read_int(H5File file, std::string key, unsigned int * data) {
+ DataSet ds = file.openDataSet(key);
+ ds.read(data, PredType::STD_U32LE);
+ ds.close();
+}
+
+void read_double(H5File file, std::string key, double * data) {
+ DataSet ds = file.openDataSet(key);
+ ds.read(data, PredType::IEEE_F64LE);
+ ds.close();
+}
+
+
+/* Return a vector containing all cycles to execute by reading a data file */
+std::vector get_cycles_list(std::string path) {
+ std::ifstream file_stream(path);
+ std::stringstream string_stream;
+ string_stream << file_stream.rdbuf();
+
+ std::string cycle_str;
+ std::vector cycles_list = {};
+
+ while(string_stream >> cycle_str) {
+ cycles_list.push_back(std::stoi(cycle_str));
+ }
+
+ return cycles_list;
+}
+
+int test_cycle(H5File file, int cycle, std::string version, vfc_probes * probes) {
+
+ /* Read the data */
+
+ std::string group = "cycle_" + std::to_string(cycle);
+
+ // This will result in the same string as group but with the cycle number
+ // being zero-padded. This is used when calling vfc_put_probe later on.
+ std::string zero_padded_group = std::to_string(cycle);
+ zero_padded_group = "cycle_" +
+ std::string(5 - zero_padded_group.length(), '0') + zero_padded_group;
+
+ try{
+ file.openGroup(group);
+ } catch(H5::Exception& e){
+ std::cerr << "group " << group << "not found" << std::endl;
+ return 0;
+ }
+
+ unsigned int dim, nupdates, col, i, j;
+ read_int(file, group + "/slater_matrix_dim", &dim);
+ read_int(file, group + "/nupdates", &nupdates);
+
+
+ double * slater_matrix = new double[dim*dim];
+ read_double(file, group + "/slater_matrix", slater_matrix);
+
+ double * slater_inverse = new double[dim*dim];
+ read_double(file, group + "/slater_inverse", slater_inverse);
+ //slater_inverse = transpose(slater_inverse, dim);
+
+ unsigned int * col_update_index = new unsigned int[nupdates];
+ read_int(file, group + "/col_update_index", col_update_index);
+
+ double * updates = new double[nupdates*dim];
+ read_double(file, group + "/updates", updates);
+
+ double * u = new double[nupdates*dim];
+
+ /* Test */
+#ifdef DEBUG
+ showMatrix(slater_matrix, dim, "OLD Slater");
+#endif
+
+#ifdef DEBUG
+ showMatrix(slater_inverse, dim, "OLD Inverse");
+#endif
+
+ for (j = 0; j < nupdates; j++) {
+ for (i = 0; i < dim; i++) {
+ col = col_update_index[j];
+ u[i + j*dim] = updates[i + j*dim] - slater_matrix[i*dim + (col - 1)];
+ slater_matrix[i*dim + (col - 1)] = updates[i + j*dim];
+ }
+ }
+
+ if (version == "maponia3") {
+ MaponiA3(slater_inverse, dim, nupdates, u, col_update_index);
+ } else if (version == "sm1") {
+ SM1(slater_inverse, dim, nupdates, u, col_update_index);
+ } else if (version == "sm2") {
+ SM2(slater_inverse, dim, nupdates, u, col_update_index);
+ } else if (version == "sm3") {
+ SM3(slater_inverse, dim, nupdates, u, col_update_index);
+ } else {
+ std::cerr << "Unknown version " << version << std::endl;
+ exit(1);
+ }
+
+#ifdef DEBUG
+ showMatrix(slater_matrix, dim, "NEW Slater");
+#endif
+
+#ifdef DEBUG
+ showMatrix(slater_inverse, dim, "NEW Inverse");
+#endif
+
+ double * res = new double[dim*dim] {0};
+ matMul(slater_matrix, slater_inverse, res, dim);
+ bool ok = is_identity(res, dim, 1e-3);
+
+ double res_max = residual_max(res, dim);
+ double res2 = residual2(res, dim);
+
+#ifdef DEBUG
+ showMatrix(res, dim, "Result");
+#endif
+
+ vfc_put_probe(probes, &(zero_padded_group)[0], &("res_max_" + version)[0], res_max);
+ vfc_put_probe(probes, &(zero_padded_group)[0], &("res2_" + version)[0], res2);
+
+ delete [] res, updates, u, col_update_index,
+ slater_matrix, slater_inverse;
+
+ return ok;
+}
+
+int main(int argc, char **argv) {
+ if (argc != 3) {
+ std::cerr << "Execute from within '/'" << std::endl;
+ std::cerr << "usage: test_h5 " << std::endl;
+ return 1;
+ }
+ std::string version(argv[1]);
+ std::vector cycles_list = get_cycles_list(argv[2]);
+ H5File file(FILE_NAME, H5F_ACC_RDONLY);
+
+ vfc_probes probes = vfc_init_probes();
+ probes = vfc_init_probes();
+
+ bool ok;
+ for (int i = 0; i < cycles_list.size(); i++) {
+ ok = test_cycle(file, cycles_list[i], version, &probes);
+ if (ok) {
+ std::cout << "ok -- cycle " << std::to_string(i)
+ << std::endl;
+ }
+ else {
+ std::cerr << "failed -- cycle " << std::to_string(i)
+ << std::endl;
+ }
+ }
+
+ vfc_dump_probes(&probes);
+
+ return ok;
+}
diff --git a/tools/extract-from-h5.py b/tools/extract-from-h5.py
new file mode 100644
index 0000000..6907be6
--- /dev/null
+++ b/tools/extract-from-h5.py
@@ -0,0 +1,72 @@
+#!/usr/bin/env python
+import h5py
+import sys
+
+# Helper script to extract a few cycles from a large dataset. This will be
+# especially useful for the Verificarlo CI, since vfc_ci_cycles.txt can be
+# used to both extract (with this script), and read the small dataset (in a CI
+# run).
+
+
+ # Parse arguments
+
+if len(sys.argv) != 4:
+ sys.stderr.write(
+ "Error: Wrong number of arguments. Usage : extract_h5.py "\
+ " \n"
+ )
+ exit(1)
+
+source_dataset_path = sys.argv[1]
+cycles_list_path = sys.argv[2]
+destination_dataset_path = sys.argv[3]
+
+
+ # Read the cycles list
+
+cycles_list = []
+
+try:
+ f = open(cycles_list_path)
+ for line in f:
+ cycles_list.extend([cycle for cycle in line.split()])
+except IOError:
+ sys.stderr.write("Error: Could not read " + cycles_list_path + "\n")
+ exit(1)
+finally:
+ f.close()
+
+
+ # Read the source dataset, and extract the cycles to the destination dataset
+
+try:
+ fs = h5py.File(source_dataset_path, "r")
+
+except IOError:
+ sys.stderr.write("Error: Could not read " + source_dataset_path + "\n")
+ exit(1)
+
+fd = h5py.File(destination_dataset_path, "w")
+
+# Copy cycles groups
+
+groups = [
+ "slater_matrix_dim",
+ "nupdates",
+ "slater_matrix",
+ "slater_inverse",
+ "col_update_index",
+ "updates"
+]
+
+for cycle in cycles_list:
+ cycle_name = "cycle_" + cycle
+
+ new_cycle = fd.create_group(cycle_name)
+
+ # Copy all datasets
+ for group_name in groups:
+ fs.copy(cycle_name + "/" + group_name, new_cycle)
+
+
+print("Dataset successfully exported to %s" % source_dataset_path)
diff --git a/vfc_ci b/vfc_ci
new file mode 100755
index 0000000..be0afdb
--- /dev/null
+++ b/vfc_ci
@@ -0,0 +1,199 @@
+#!/usr/bin/env python3
+
+# This is the entry point of the Verificarlo CI command line interface, which is
+# based on argparse and this article :
+# https://mike.depalatis.net/blog/simplifying-argparse.html
+# From here, 3 subcommands can be called :
+# - setup : create a vfc_ci branch and workflow on the current Git repo
+# - test : run and export test results according to the vfc_tests_config.json
+# - serve : launch a Bokeh server to visualize run results
+
+import argparse
+
+##########################################################################
+
+# Parameters validation helpers
+
+
+def is_port(string):
+ value = int(string)
+ if value < 0 or value > 65535:
+ raise argparse.ArgumentTypeError("Value has to be between 0 and 65535")
+ return value
+
+
+def is_directory(string):
+ import os
+
+ isdir = os.path.isdir(string)
+ if not isdir:
+ raise argparse.ArgumentTypeError("Directory does not exist")
+
+ return string
+
+
+##########################################################################
+
+ # Subcommand decorator
+
+cli = argparse.ArgumentParser(
+ description="Define, run, automatize, and visualize custom Verificarlo tests."
+)
+subparsers = cli.add_subparsers(dest="subcommand")
+
+
+def subcommand(description="", args=[], parent=subparsers):
+ def decorator(func):
+ parser = parent.add_parser(func.__name__, description=description)
+ for arg in args:
+ parser.add_argument(*arg[0], **arg[1])
+ parser.set_defaults(func=func)
+ return decorator
+
+
+def argument(*name_or_flags, **kwargs):
+ return ([*name_or_flags], kwargs)
+
+
+##########################################################################
+
+ # "setup" subcommand
+
+@subcommand(
+ description="Create an automated workflow to execute Verificarlo tests.",
+ args=[
+ argument(
+ "git_host",
+ help="""
+ specify where your repository is hosted
+ """,
+ choices=["github", "gitlab"]
+ )
+ ]
+)
+def setup(args):
+ import ci.setup
+ ci.setup.setup(args.git_host)
+
+ # "test" subcommand
+
+
+@subcommand(
+ description="Execute predefined Verificarlo tests and save their results.",
+ args=[
+ argument(
+ "-g", "--is-git-commit",
+ help="""
+ When specified, the last Git commit of the local repository (working
+ directory) will be fetched and associated with the run.
+ """,
+ action="store_true"
+ ),
+ argument(
+ "-r", "--export-raw-results",
+ help="""
+ Specify if an additional HDF5 file containing the raw results must be
+ exported.
+ """,
+ action="store_true"
+ ),
+ argument(
+ "-d", "--dry-run",
+ help="""
+ Perform a dry run by not saving the test results.
+ """,
+ action="store_true"
+ )
+ ]
+)
+def test(args):
+ import ci.test
+ ci.test.run(args.is_git_commit, args.export_raw_results, args.dry_run)
+
+ # "serve" subcommand
+
+
+@subcommand(
+ description="""
+ Start a server to visualize Verificarlo test results.
+ """,
+ args=[
+ argument(
+ "-s", "--show",
+ help="""
+ Specify if the report must be opened in the browser at server
+ startup.
+ """,
+ action="store_true"
+ ),
+ argument(
+ "-gd", "--git-directory",
+ help="""
+ Path to a local Git repository. The report will be linked to the
+ remote URL (GitHub and GitLab are supported).
+ """,
+ type=is_directory
+ ),
+ argument(
+ "-gu", "--git-url",
+ help="""
+ GitHub or GitLab repository URL. The report will be linked to this
+ URL.
+ """,
+ type=str
+ ),
+ argument(
+ "-p", "--port",
+ help="""
+ The port on which the server will run. Defaults to 8080.
+ """,
+ type=is_port,
+ default=8080
+ ),
+ argument(
+ "-a", "--allow-origin",
+ help="""
+ The origin (URL) from which the report will be accessible.
+ Port number must not be specified. Defaults to * (allow everything).
+ """,
+ type=str,
+ default="*"
+ ),
+ argument(
+ "-l", "--logo",
+ help="""
+ Specify the URL of an image to be displayed in the report header.
+ """,
+ type=str
+ )
+ ]
+)
+def serve(args):
+
+ # git_directory and git_url are supposed to be exclusive
+ if args.git_directory is not None and args.git_url is not None:
+ raise argparse.ArgumentTypeError(
+ "\"-gd\" / \"--git-directory\" and \"-gu\" / \"--git-url\" are "
+ "mutually exclusive. Please make sure to use at most one of them."
+ )
+
+ import ci.serve
+ ci.serve.serve(
+ args.show,
+ args.git_directory,
+ args.git_url,
+ args.port,
+ args.allow_origin,
+ args.logo
+ )
+
+
+###############################################################################
+
+ # Main command group and entry point
+if __name__ == "__main__":
+ args = cli.parse_args()
+ if args.subcommand is None:
+ cli.print_help()
+ else:
+ args.func(args)
diff --git a/vfc_ci_cycles.txt b/vfc_ci_cycles.txt
new file mode 100644
index 0000000..840505a
--- /dev/null
+++ b/vfc_ci_cycles.txt
@@ -0,0 +1,2 @@
+1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25
+327 655 983 1311 1639 1967 2295 2623 2951 3279 3607 3935 4263 4591 4919 5247 5575 5903 6231 6559 6887 7215 7543 7871 8199
diff --git a/vfc_tests_config.json b/vfc_tests_config.json
new file mode 100644
index 0000000..d036855
--- /dev/null
+++ b/vfc_tests_config.json
@@ -0,0 +1,92 @@
+{
+ "make_command": "make -f Makefile.verificarlo",
+ "executables": [
+ {
+ "executable": "bin/vfc_test_h5",
+ "parameters" : "maponia3 vfc_ci_cycles.txt",
+ "vfc_backends": [
+ {
+ "name": "libinterflop_mca.so",
+ "repetitions": 50
+ }
+ ]
+ },
+
+ {
+ "executable": "bin/vfc_test_h5",
+ "parameters" : "sm1 vfc_ci_cycles.txt",
+ "vfc_backends": [
+ {
+ "name": "libinterflop_mca.so",
+ "repetitions": 50
+ }
+ ]
+ },
+
+ {
+ "executable": "bin/vfc_test_h5",
+ "parameters" : "sm2 vfc_ci_cycles.txt",
+ "vfc_backends": [
+ {
+ "name": "libinterflop_mca.so",
+ "repetitions": 50
+ }
+ ]
+ },
+
+ {
+ "executable": "bin/vfc_test_h5",
+ "parameters" : "sm3 vfc_ci_cycles.txt",
+ "vfc_backends": [
+ {
+ "name": "libinterflop_mca.so",
+ "repetitions": 50
+ }
+ ]
+ },
+
+ {
+ "executable": "bin/vfc_test_h5",
+ "parameters" : "maponia3 vfc_ci_cycles.txt",
+ "vfc_backends": [
+ {
+ "name": "libinterflop_mca.so --mode=rr",
+ "repetitions": 50
+ }
+ ]
+ },
+
+ {
+ "executable": "bin/vfc_test_h5",
+ "parameters" : "sm1 vfc_ci_cycles.txt",
+ "vfc_backends": [
+ {
+ "name": "libinterflop_mca.so --mode=rr",
+ "repetitions": 50
+ }
+ ]
+ },
+
+ {
+ "executable": "bin/vfc_test_h5",
+ "parameters" : "sm2 vfc_ci_cycles.txt",
+ "vfc_backends": [
+ {
+ "name": "libinterflop_mca.so --mode=rr",
+ "repetitions": 50
+ }
+ ]
+ },
+
+ {
+ "executable": "bin/vfc_test_h5",
+ "parameters" : "sm3 vfc_ci_cycles.txt",
+ "vfc_backends": [
+ {
+ "name": "libinterflop_mca.so --mode=rr",
+ "repetitions": 50
+ }
+ ]
+ }
+ ]
+}