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better documentation
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@ -31,8 +31,12 @@ For more details, see the corresponding part of the [Python documentation](https
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1. Download the latest source code distribution (in `.tar.gz` format) of the TREXIO Python API
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1. Download the latest source code distribution (in `.tar.gz` format) of the TREXIO Python API
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2. Unpack and `cd` in the output directory
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2. Unpack and `cd` in the output directory
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3. Run `pip3 install -r requirements.txt` (this installs all python dependencies)
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3. Run `pip3 install -r requirements.txt` (this installs all python dependencies)
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4. Run `pip3 install .` (this installs `trexio` in your environment)
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4. Export custom environment variables needed for the installation. Steps 1 and 2 can be skipped if HDF5 is properly configured for `pkg-config` (i.e. if executing `pkg-config --libs hdf5` returns a list of options).
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5. Run `cd test && python3 test_api.py` (this executes several tests that verify the installation)
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1. `export H5_CFLAGS=-I/path/to/hdf5/include`
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2. `export H5_LDFLAGS=-L/path/to/hdf5/lib`
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3. `source tools/set_NUMPY_INCLUDEDIR.sh`
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5. Run `pip3 install .` (this installs `trexio` in your environment)
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6. Run `cd test && python3 test_api.py` (this executes several tests that verify the installation)
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You are ready to go!
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You are ready to go!
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@ -54,8 +58,9 @@ The example notebook can be launched using the following command:
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#### Additional steps needed to run a custom virtual environment in Jupyter notebooks
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#### Additional steps needed to run a custom virtual environment in Jupyter notebooks
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If you have installed `trexio` in a virtual environemnt called, e.g. `myvenv`, but would like to use your system-wide Jupyter installation, this is also possible.
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In some cases, it may happen that the Jupyter kernels in the activated virtual environment (e.g. `myvenv`) still point to the system-wide python binaries and not to the environment ones.
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This requires `ipykernel` python package to be installed, which usually comes together with the Jupyter installation. If this is not the case, run `pip install ipykernel`.
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This will result in `ImportError` when importing `trexio` in the notebook cell. In order to avoid this, the `myvenv` has to be installed as an additional kernel.
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This requires `ipykernel` python package, which usually comes together with the Jupyter installation. If this is not the case, run `pip install ipykernel`.
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You can install `myvenv` as a kernel by executing the following command:
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You can install `myvenv` as a kernel by executing the following command:
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`python3 -m ipykernel install --user --name=myvenv`
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`python3 -m ipykernel install --user --name=myvenv`
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@ -1,24 +0,0 @@
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# Additional information related to the installation of the TREXIO Python API
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Removing MANIFEST.in leads to issues in the installation. In particular, the .c and .h source files do not get copied
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from the src/ directory into the tar.gz which is produced by setup sdist command.
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These source files are required to build the pytrexio.so extension module, which is needed for the Python API.
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Then the following commands do the job of installing trexio in virtual environment:
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$ python3 -m pip install --upgrade setuptools wheel twine
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$ python3 -s setup.py --no-user-cfg build
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$ python3 setup.py sdist bdist_wheel
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$ python3 -m pip install dist/trexio-0.1-*.whl --force-reinstall
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BUG: when trying to install trexio from tar.gz, trexio appears to be installed
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after user runs [python3 -s setup.py --no-user-cfg build]
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but before [python3 -m pip install dist/{WHEELNAME}.whl]
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which leads to pip install saying that trexio is already installed but the test fails saying that _trexio was not found,
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indicating that probably first installation did not go well.
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FIX: Use --force-reinstall option with pip install
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The installed in virtual environment trexio can be uninstalled using [pip uninstall trexio]
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but only from the root directory where the initially used (to install) setup.py script is located.
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For example, it is most probably the python/ directory of the TREXIO_ROOT folder.
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@ -6,8 +6,6 @@ set -e
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H5_CFLAGS_LOCAL=$1
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H5_CFLAGS_LOCAL=$1
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H5_LDFLAGS_LOCAL=$2
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H5_LDFLAGS_LOCAL=$2
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# This script should update the version of the Python package
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#source version.py
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# Install/upgrade packages required for the installation
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# Install/upgrade packages required for the installation
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python3 -m pip install --upgrade setuptools wheel twine
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python3 -m pip install --upgrade setuptools wheel twine
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@ -33,23 +31,21 @@ python3 -m pip install dist/trexio-*.whl --force-reinstall
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# Run the command below in the root directory to install the package in 'editable' (-e) mode without dependencies (--no-deps)
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# Run the command below in the root directory to install the package in 'editable' (-e) mode without dependencies (--no-deps)
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#python -m pip install -e . --no-deps
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#python -m pip install -e . --no-deps
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# Uninstall pytrexio: this only works from the pytrexio root directory (more likely python/ folder) and only after --force-reinstall
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# Uninstall pytrexio: this only works from the pytrexio root directory
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#python3 -m pip uninstall trexio
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#python3 -m pip uninstall trexio
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# Test the current release by uploading to TestPyPI sandbox
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# Test the current release by uploading to TestPyPI sandbox
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#python3 -m twine upload --repository testpypi dist/trexio-*.tar.gz
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#python3 -m twine upload --repository testpypi dist/trexio-*.tar.gz
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# NOTE:I get an error:
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# Binary wheel 'trexio-0.1-cp38-cp38-linux_x86_64.whl' has an unsupported platform tag 'linux_x86_64'.
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# when uploading the wheel instead of the tar.gz file to testpypi
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# This is a well-known issue, see https://stackoverflow.com/questions/59451069/binary-wheel-cant-be-uploaded-on-pypi-using-twine
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# Once fixed both .tar.gz and .whl distribution can be uploaded, meaning that dist/trexio-*.tar.gz can be replaced by dist/*
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#
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# Compatibility tags for Linux have been discussed in PEP-513 https://www.python.org/dev/peps/pep-0513/
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# Upload updated version of PyTREXIO to PyPI
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# Upload updated version of PyTREXIO to PyPI
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#python3 -m twine upload dist/trexio-*.tar.gz
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#python3 -m twine upload dist/trexio-*.tar.gz
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# Cleaning
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# Cleaning
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rm -rf build dist trexio.egg-info
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rm -rf build dist trexio.egg-info
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# Additional information related to the installation of the TREXIO Python API
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#Removing MANIFEST.in leads to issues in the installation. In particular, the .c and .h source files do not get copied
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#from the src/ directory into the tar.gz which is produced by setup sdist command.
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#These source files are required to build the pytrexio.so extension module, which is needed for the Python API.
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