Merge pull request #368 from BvB93/master

ENH: Add a workflow for creating manylinyx2014 wheels

.github/workflows/pypi.yaml

@@ -3,37 +3,162 @@ name: Publish
 on:
   release:
     types: [published]
+  workflow_dispatch:
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.head_ref || github.run_id }}
+  cancel-in-progress: true
+
+defaults:
+  run:
+    shell: bash
 
 jobs:
-  build:
-    name: Build wheels
-    runs-on: ubuntu-latest
+  build_wheels:
+    name: Build wheels ${{ matrix.version }}-${{ matrix.buildplat[1] }}
+    runs-on: ${{ matrix.buildplat[0] }}
+    strategy:
+      fail-fast: false
+      matrix:
+        buildplat:
+        - [ubuntu-20.04, manylinux_x86_64]
+        version:
+        - "cp37"
+        - "cp38"
+        - "cp39"
+        - "cp310"
+
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
+
+      - name: Build wheels
+        uses: pypa/[email protected]
+        env:
+          CIBW_BUILD: ${{ matrix.version }}-${{ matrix.buildplat[1] }}
 
-      - name: Setup conda
-        uses: s-weigand/setup-conda@v1
+      - uses: actions/upload-artifact@v3
         with:
-          update-conda: false
+          name: wheels
+          path: ./wheelhouse/*.whl
+
+  build_sdist:
+    name: Build wheels sdist
+    runs-on: ubuntu-latest
+    env:
+      QMFLOWS_INCLUDEDIR: ""
+      QMFLOWS_LIBDIR: ""
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Set up Python
+        uses: actions/setup-python@v3
 
       - name: Install dependencies
-        run: conda create -n test -c conda-forge boost eigen libint==2.6.0 highfive Cython setuptools wheel "pybind11>=2.2.4"
+        run: pip install Cython "setuptools>=48.0" wheel "pybind11>=2.2.4"
 
-      - name: Conda info
+      - name: Python info
         run: |
-          source $CONDA/bin/activate test
-          conda info
+          which python
+          python --version
 
-      - name: Conda list
-        run: conda list -n test
+      - name: Installed packages
+        run: pip list
 
-      - name: Build wheels
+      - name: Build sdist
         run: |
-          source $CONDA/bin/activate test
           python setup.py sdist
+          tree dist
+
+      - uses: actions/upload-artifact@v3
+        with:
+          name: wheels
+          path: ./dist/*.tar.gz
+
+  test_sdist:
+    name: Test wheels sdist
+    runs-on: ubuntu-latest
+    needs: [build_sdist]
+    steps:
+    - uses: actions/checkout@v3
+
+    - name: Install CP2K
+      run: bash scripts/download_cp2k.sh 9.1
+
+    - name: Info CP2K
+      run: cp2k.popt --version
+
+    - name: Setup conda
+      uses: s-weigand/setup-conda@v1
+      with:
+        update-conda: true
+
+    - uses: actions/download-artifact@v3
+      with:
+        name: wheels
+        path: dist
+
+    - name: Install dependencies
+      run: |
+        conda install -c conda-forge boost eigen libint==2.6.0 highfive
+        cd dist
+        pip install *.tar.gz -v
+        pip install -r ../test_requirements.txt
+
+    - name: Conda info
+      run: conda info
+
+    - name: Conda list
+      run: conda list
+
+    - name: Test with pytest
+      run: |
+        mkdir /tmp/nanoqm
+        cp setup.cfg /tmp/nanoqm/
+        cp conftest.py /tmp/nanoqm/conftest.py
+        cp -r test /tmp/nanoqm/test
+        cd /tmp/nanoqm
+        pytest -m "not (slow or long)"
+
+  upload_wheels:
+    name: Upload wheels
+    runs-on: ubuntu-latest
+    needs: [test_sdist, build_wheels]
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: actions/download-artifact@v3
+        with:
+          name: wheels
+          path: dist
+
+      - name: Set up Python
+        uses: actions/setup-python@v3
+
+      - name: Install dependencies
+        run: pip install twine
+
+      - name: Python info
+        run: |
+          which python
+          python --version
+
+      - name: Installed packages
+        run: pip list
+
+      - name: Validate wheels
+        run: |
+          tree dist
+          twine check dist/*
 
       - name: Publish wheels
         uses: pypa/gh-action-pypi-publish@master
         with:
           user: __token__
           password: ${{ secrets.PYPI_TOKEN }}
+
+      - name: Attach wheels to GitHub release
+        if: github.event_name == 'release'
+        uses: AButler/[email protected]
+        with:
+          files: 'dist/*'
+          repo-token: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/pythonapp.yml

@@ -80,18 +80,7 @@ jobs:
     - uses: actions/checkout@v3
 
     - name: Install CP2K
-      run: |
-        version="${{ matrix.cp2k }}"
-        version_long=v"${{ matrix.cp2k }}".0
-
-        git clone https://github.com/cp2k/cp2k
-        cd cp2k
-        git checkout tags/$version_long
-        ln -s data /usr/share/cp2k
-
-        wget -nv https://github.com/cp2k/cp2k/releases/download/$version_long/cp2k-$version-Linux-x86_64.ssmp -O cp2k.ssmp
-        chmod u+rx cp2k.ssmp
-        mv cp2k.ssmp /usr/local/bin/cp2k.popt
+      run: bash scripts/download_cp2k.sh "${{ matrix.cp2k }}"
 
     - name: Info CP2K
       run: cp2k.popt --version
@@ -122,12 +111,13 @@ jobs:
         source $CONDA/bin/activate test
         case "${{ matrix.pre_release }}" in
           "true")
-            pip install --pre -r ./test_requirements.txt --upgrade --force-reinstall
+            pip install --pre -r ./install_requirements.txt -r ./test_requirements.txt --upgrade --force-reinstall
             pip install git+https://github.com/SCM-NV/qmflows@master --upgrade
             pip uninstall plams -y; pip install git+https://github.com/SCM-NV/PLAMS@master --upgrade
             pip install git+https://github.com/NLeSC/noodles@master --upgrade
             ;;
           *)
+            pip install -r ./install_requirements.txt
             pip install -r ./test_requirements.txt
             ;;
         esac
@@ -143,7 +133,7 @@ jobs:
     - name: Install the package
       run: |
         source $CONDA/bin/activate test
-        pip install -e . -vvv
+        pip install -e . -vvv --no-deps
 
     - name: Test with pytest
       run: |

MANIFEST.in

@@ -0,0 +1,13 @@
+exclude test/*
+include *_requirements.txt
+
+include licenses/*.txt
+include licenses/*.rst
+
+include nanoqm/py.typed
+recursive-include nanoqm *.pyi
+include nanoqm/basis/GTH_POTENTIALS
+include nanoqm/basis/*.json
+include nanoqm/basis/BASIS_*
+
+include libint/include/*.hpp

README.rst

@@ -22,17 +22,25 @@ For further information on the theory behind nano-qmflows and how to use the pro
 Installation
 ------------
 
-In order to install the **nano-qmflows** library you need to install *Miniconda* as detailed here_.
+In order to install the **nano-qmflows** library there two options:
+
+1. Install pre-compiled binaries.
+2. Build Nano-QMFlows from source.
+
+Pre-compiled linux binaries are available on pypi. In order to use them all one needs is a linux machine and then issue the ``pip install nano-qmflows`` command.
+
+On the other hand, other operating systems (and source builds in general) first require an installation of *Miniconda* as is detailed here_.
 
 .. _here: https://docs.conda.io/en/latest/miniconda.html
 
-Then,  to install the **nano-qmflows** library type the following commands inside the conda environment:
-  - ``conda create -n qmflows -c conda-forge boost eigen libint==2.6.0 highfive``
-  - ``conda activate qmflows``
-  - ``pip install nano-qmflows --upgrade``
+Then, to install the **nano-qmflows** library type the following commands inside the conda environment:
+
+- ``conda create -n qmflows -c conda-forge boost eigen libint==2.6.0 highfive``
+- ``conda activate qmflows``
+- ``pip install nano-qmflows --upgrade``
 
 .. note::
-   For GCC <7 one has to pass ``eigen=3.3``.
+   Older compilers, such as GCC <7, might not be compatible with the latest ``eigen`` version and require specification of *.e.g* ``eigen=3.3``.
 
 Advantages and Limitations
 --------------------------

install_requirements.txt

@@ -0,0 +1,12 @@
+h5py
+mendeleev
+more-itertools
+noodles>=0.3.3
+numpy
+scipy
+schema
+pyyaml>=5.1
+plams>=1.5.1
+qmflows>=0.12.0
+packaging>=1.16.8
+Nano-Utils>=2.0.0

licenses/README.rst

@@ -0,0 +1,3 @@
+Licenses for various third-party binaries distributed in the Nano-QMFlows wheels.
+
+Note that no such files are present in source-only Nano-QMFlows distributions.

licenses/hdf5.txt

@@ -0,0 +1,74 @@
+Copyright Notice and License Terms for
+HDF5 (Hierarchical Data Format 5) Software Library and Utilities
+-----------------------------------------------------------------------------
+
+HDF5 (Hierarchical Data Format 5) Software Library and Utilities
+Copyright 2006 by The HDF Group.
+
+NCSA HDF5 (Hierarchical Data Format 5) Software Library and Utilities
+Copyright 1998-2006 by The Board of Trustees of the University of Illinois.
+
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without modification, are permitted for any
+purpose (including commercial purposes) provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this list of conditions, and
+the following disclaimer.
+2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions,
+and the following disclaimer in the documentation and/or materials provided with the distribution.
+3. Neither the name of The HDF Group, the name of the University, nor the name of any Contributor
+may be used to endorse or promote products derived from this software without specific prior
+written permission from The HDF Group, the University, or the Contributor, respectively.
+
+DISCLAIMER:
+THIS SOFTWARE IS PROVIDED BY THE HDF GROUP AND THE CONTRIBUTORS "AS IS" WITH NO
+WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED. IN NO EVENT SHALL THE HDF GROUP OR
+THE CONTRIBUTORS BE LIABLE FOR ANY DAMAGES SUFFERED BY THE USERS ARISING OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+You are under no obligation whatsoever to provide any bug fixes, patches, or upgrades to the features,
+functionality or performance of the source code ("Enhancements") to anyone; however, if you choose
+to make your Enhancements available either publicly, or directly to The HDF Group, without imposing a
+separate written license agreement for such Enhancements, then you hereby grant the following
+license: a non-exclusive, royalty-free perpetual license to install, use, modify, prepare derivative works,
+incorporate into other computer software, distribute, and sublicense such enhancements or derivative
+works thereof, in binary and source code form.
+
+Limited portions of HDF5 were developed by Lawrence Berkeley National Laboratory (LBNL). LBNL's
+Copyright Notice and Licensing Terms can be found here: COPYING_LBNL_HDF5 file in this directory or
+at http://support.hdfgroup.org/ftp/HDF5/releases/COPYING_LBNL_HDF5.
+
+Contributors: National Center for Supercomputing Applications (NCSA) at the University of Illinois,
+Fortner Software, Unidata Program Center (netCDF), The Independent JPEG Group (JPEG), Jean-loup
+Gailly and Mark Adler (gzip), and Digital Equipment Corporation (DEC).
+
+Portions of HDF5 were developed with support from the Lawrence Berkeley National Laboratory (LBNL)
+and the United States Department of Energy under Prime Contract No. DE-AC02-05CH11231.
+
+Portions of HDF5 were developed with support from Lawrence Livermore National Laboratory and the
+United States Department of Energy under Prime Contract No. DE-AC52-07NA27344.
+
+Portions of HDF5 were developed with support from the University of California, Lawrence Livermore
+National Laboratory (UC LLNL). The following statement applies to those portions of the product and
+must be retained in any redistribution of source code, binaries, documentation, and/or accompanying
+materials:
+
+This work was partially produced at the University of California, Lawrence Livermore National
+Laboratory (UC LLNL) under contract no. W-7405-ENG-48 (Contract 48) between the U.S. Department
+of Energy (DOE) and The Regents of the University of California (University) for the operation of UC
+LLNL.
+
+DISCLAIMER:
+THIS WORK WAS PREPARED AS AN ACCOUNT OF WORK SPONSORED BY AN AGENCY OF THEUNITED
+STATES GOVERNMENT. NEITHER THE UNITED STATES GOVERNMENT NOR THE UNIVERSITY OF
+CALIFORNIA NOR ANY OF THEIR EMPLOYEES, MAKES ANY WARRANTY, EXPRESS OR IMPLIED, OR
+ASSUMES ANY LIABILITY OR RESPONSIBILITY FOR THE ACCURACY, COMPLETENESS, OR USEFULNESS OF
+ANY INFORMATION, APPARATUS, PRODUCT, OR PROCESS DISCLOSED, OR REPRESENTS THAT ITS USE
+WOULD NOT INFRINGE PRIVATELY- OWNED RIGHTS. REFERENCE HEREIN TO ANY SPECIFIC
+COMMERCIAL PRODUCTS, PROCESS, OR SERVICE BY TRADE NAME, TRADEMARK, MANUFACTURER, OR
+OTHERWISE, DOES NOT NECESSARILY CONSTITUTE OR IMPLY ITS ENDORSEMENT, RECOMMENDATION,
+OR FAVORING BY THE UNITED STATES GOVERNMENT OR THE UNIVERSITY OF CALIFORNIA. THE VIEWS
+AND OPINIONS OF AUTHORS EXPRESSED HEREIN DO NOT NECESSARILY STATE OR REFLECT THOSE OF
+THE UNITED STATES GOVERNMENT OR THE UNIVERSITY OF CALIFORNIA, AND SHALL NOT BE USED FOR
+ADVERTISING OR PRODUCT ENDORSEMENT PURPOSES.

licenses/libint.txt

@@ -0,0 +1,17 @@
+Libint - a library for the evaluation of molecular integrals of many-body operators over Gaussian functions
+
+Copyright (C) 2004-2020 Edward F. Valeev
+
+Libint is free software. Most of the source code of the Libint compiler (code generator)
+can be redistributed and/or modified under the terms of the GNU General Public License, version 3,
+as published by the Free Software Foundation (see the accompanying file COPYING;
+if you did not receive this file refer to <http://www.gnu.org/licenses/>).
+The rest of Libint, including the generated source, can be distributed under
+the GNU Lesser General Public License, version 3, (see the file COPYING.LESSER,
+or <http://www.gnu.org/licenses/>). The applicable license is specified in each
+source file. If not indicated, the applicable license is GNU LGPL, version 3 (not GPL).
+
+Libint is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.