[python-package] add py312 (#50) workaround

* [pyproject.toml] change dependency order s.t. legacy dep resolver installs mdtraj after bezier 
* [README and installation.rst] Add instructions/admonition for Python 3.12 users
* [workflows] separate tests for py312 from the rest

Author: gph82

.github/workflows/python-package.macos.yml

@@ -1,7 +1,7 @@
 # This workflow will install Python dependencies, run tests and lint with a variety of Python versions
 # For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
 
-name: Python [3.7,3.8,3.9,3.10,3.11] MacOs
+name: Python [3.7,3.8,3.9,3.10,3.11,3.12] MacOs
 
 on:
   push:
@@ -23,7 +23,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [macos-latest]
-        python-version: [3.7, 3.8, 3.9, '3.10', '3.11']
+        python-version: [3.7, 3.8, 3.9, '3.10', '3.11','3.12']
         # Proposed workaround for legacy versions, see
         # https://github.com/actions/setup-python/issues/856 and
         # https://github.com/actions/runner-images/issues/9770#issuecomment-2085623315
@@ -44,24 +44,22 @@ jobs:
       run: |
         python -m pip install --upgrade pip
         pip install flake8 pytest pytest-cov pytest-xdist
-   #    if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
-    - name: Install package
+    - name: Install package Python lt 3.12
+      if: matrix.python-version != '3.12' 
       run: |
         pip install --upgrade pip
         pip install --upgrade setuptools
         pip install -e .
         pip freeze
-    #- name: Lint with flake8
-    #  run: |
-    #    # stop the build if there are Python syntax errors or undefined names
-    #    flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
-    #    # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
-    #    flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
-    #- name: Test with pytest and coverage MacOs one single thread and ignoring calls to scripts (WIP)
-    #  if: runner.os == 'macOs'
-    #  run: |
-    #    pytest -vs --cov=./ --cov-report=xml --disable-warnings --ignore-glob="test_scripts.py"
-    # if: runner.os == 'macOs'
+    - name: Install package Python eq 3.12
+      if: matrix.python-version == '3.12' 
+      run: |
+        pip install --upgrade pip
+        pip install --upgrade setuptools
+        pip install bezier
+        pip install mdtraj --use-deprecated=legacy-resolver
+        pip install -e . --use-deprecated=legacy-resolver
+        pip freeze
     - name: Test with pytest and coverage macos
       continue-on-error: true
       run: |

.github/workflows/python-package.yml

@@ -1,7 +1,7 @@
 # This workflow will install Python dependencies, run tests and lint with a variety of Python versions
 # For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
 
-name: Python [3.7,3.8,3.9,3.10,3.11] Linux
+name: Python [3.7,3.8,3.9,3.10,3.11,3.12] Linux
 
 on:
   push:
@@ -21,7 +21,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-latest]
-        python-version: [3.7, 3.8, 3.9, '3.10', '3.11']
+        python-version: [3.7, 3.8, 3.9, '3.10', '3.11','3.12']
 
     steps:
     - uses: actions/checkout@v4
@@ -32,25 +32,23 @@ jobs:
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        pip install flake8 pytest pytest-cov pytest-xdist
-   #    if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
-    - name: Install package
+        pip install pytest pytest-cov pytest-xdist
+    - name: Install package Python lt 3.12
+      if: matrix.python-version != '3.12' 
       run: |
         pip install --upgrade pip
         pip install --upgrade setuptools
         pip install -e .
         pip freeze
-    #- name: Lint with flake8
-    #  run: |
-    #    # stop the build if there are Python syntax errors or undefined names
-    #    flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
-    #    # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
-    #    flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
-    #- name: Test with pytest and coverage MacOs one single thread and ignoring calls to scripts (WIP)
-    #  if: runner.os == 'macOs'
-    #  run: |
-    #    pytest -vs --cov=./ --cov-report=xml --disable-warnings --ignore-glob="test_scripts.py"
-    # if: runner.os == 'macOs'
+    - name: Install package Python eq 3.12
+      if: matrix.python-version == '3.12' 
+      run: |
+        pip install --upgrade pip
+        pip install --upgrade setuptools
+        pip install bezier
+        pip install mdtraj --use-deprecated=legacy-resolver
+        pip install -e . --use-deprecated=legacy-resolver
+        pip freeze
     - name: Test with pytest and coverage Linux 8 threads
       run: |
         echo -e '[run]\nomit = *dihedrals.py,*contact_matrix.py' > .coveragerc

README.rst

@@ -42,14 +42,35 @@ Currently, docs are hosted at `<http://proteinformatics.org/mdciao/>`_, but this
 
 System Requirements
 ===================
-``mdciao`` is developed in GNU/Linux, and CI-tested via `github actions <https://github.com/gph82/mdciao/actions?query=workflow%3A%22Python+package%22>`_ for GNU/Linux and MacOs. Tested python versions are:
+``mdciao`` is developed in GNU/Linux, and CI-tested via `github actions <https://github.com/gph82/mdciao/actions>`_ for GNU/Linux and MacOs. Tested Python versions are:
 
 * GNU/Linux: 3.7, 3.8, 3.9, 3.10, 3.11
 * MacOs: 3.7, 3.8, 3.9, 3.10, 3.11. For Python 3.7, four CI-tests involving `mdtraj.compute_dssp <https://www.mdtraj.org/1.9.8.dev0/api/generated/mdtraj.compute_dssp.html?highlight=dssp#mdtraj.compute_dssp>`_ ,
 are skipped because of a hard to repdroduce, random segmentation fault, which apparently wont fix, see here `<https://github.com/mdtraj/mdtraj/issues/1574>`_ and  `here <https://github.com/mdtraj/mdtraj/issues/1473>`_.
 
 So everything should work *out of the box* in these conditions.
 
+.. admonition:: Python 3.12 users
+
+   If you try to install on Python 3.12, you will get a dependency error, because
+
+   * the module ``bezier`` `requires Numpy >= 2.0 for Python 3.12 <https://github.com/dhermes/bezier/releases/tag/2024.6.20>`_, but
+   * the module ``mdtraj`` `has pinned Numpy <= 2.0 <https://github.com/mdtraj/mdtraj/issues/1873/>`_.
+
+   Still, you can install mdciao in Python 3.12 **if you don't mind a somewhat inconsistent environment**:
+
+   >>> pip install bezier
+   >>> pip install mdtraj --use-deprecated=legacy-resolver
+   >>> pip install mdciao --use-deprecated=legacy-resolver
+
+   What we are doing is installing ``bezier`` normally (using ``numpy>=2.0``) and then installing ``mdtraj`` using ``pip``'s legacy resolver, which will install ``numpy-1.26.4`` even if that yields an inconsistent environment. You will get the notification:
+
+   >>> ERROR: pip's legacy dependency resolver does not consider dependency conflicts when selecting packages. This behaviour is the source of the following dependency conflicts.
+   >>> mdtraj 1.10.0 requires numpy<2.0.0a0,>=1.23, but you'll have numpy 2.0.0 which is incompatible.
+
+   Since ``mdciao`` installs and passes the CI-tests for Python 3.12 in such an environment, you can use it **at your own risk**. Please report on any issues you might find. Please note that the ``--use-deprecated=legacy-resolver`` option `might not be available in the future <https://pip.pypa.io/en/stable/user_guide/#deprecation-timeline>`_.
+
+
 Authors
 =======
 ``mdciao`` is written and maintained by Guillermo Pérez-Hernández (`ORCID <http://orcid.org/0000-0002-9287-8704>`_) currently at the `Institute of Medical Physics and Biophysics <https://biophysik.charite.de/ueber_das_institut/team/>`_ in the

doc/installation.rst

@@ -19,6 +19,26 @@ We recommend you install ``mdciao`` via the `pip <https://pypi.org/project/pip/>
 
  >>> pip install mdciao
 
+.. admonition:: Python 3.12 users
+
+   If you try to install on Python 3.12, you will get a dependency error, because
+
+   * the module ``bezier`` `requires Numpy >= 2.0 for Python 3.12 <https://github.com/dhermes/bezier/releases/tag/2024.6.20>`_, but
+   * the module ``mdtraj`` `has pinned Numpy <= 2.0 <https://github.com/mdtraj/mdtraj/issues/1873/>`_.
+
+   Still, you can install mdciao in Python 3.12 **if you don't mind a somewhat inconsistent environment**:
+
+   >>> pip install bezier
+   >>> pip install mdtraj --use-deprecated=legacy-resolver
+   >>> pip install mdciao --use-deprecated=legacy-resolver
+
+   What we are doing is installing ``bezier`` normally (using ``numpy>=2.0``) and then installing ``mdtraj`` using ``pip``'s legacy resolver, which will install ``numpy-1.26.4`` even if that yields an inconsistent environment. You will get the notification:
+
+   >>> ERROR: pip's legacy dependency resolver does not consider dependency conflicts when selecting packages. This behaviour is the source of the following dependency conflicts.
+   >>> mdtraj 1.10.0 requires numpy<2.0.0a0,>=1.23, but you'll have numpy 2.0.0 which is incompatible.
+
+   Since ``mdciao`` installs and passes the CI-tests for Python 3.12 in such an environment, you can use it **at your own risk**. Please report on any issues you might find. Please note that the ``--use-deprecated=legacy-resolver`` option `might not be available in the future <https://pip.pypa.io/en/stable/user_guide/#deprecation-timeline>`_.
+
 Getting started
 ~~~~~~~~~~~~~~~
 For the impatient, you can directly issue afterwards::
@@ -98,7 +118,7 @@ Installation from source
 
 Operating systems and Python versions
 -------------------------------------
-``mdciao`` is developed in GNU/Linux, and CI-tested via `github actions <https://github.com/gph82/mdciao/actions?query=workflow%3A%22Python+package%22>`_ for GNU/Linux and MacOs. Tested python versions are:
+``mdciao`` is developed in GNU/Linux, and CI-tested via `github actions <https://github.com/gph82/mdciao/actions>`_ for GNU/Linux and MacOs. Tested python versions are:
 
 * GNU/Linux: 3.7, 3.8, 3.9, 3.10, 3.11
 * MacOs: 3.7, 3.8, 3.9, 3.10, 3.11. For Python 3.7, four CI-tests involving `mdtraj.compute_dssp <https://www.mdtraj.org/1.9.8.dev0/api/generated/mdtraj.compute_dssp.html?highlight=dssp#mdtraj.compute_dssp>`_ ,

pyproject.toml

@@ -18,6 +18,7 @@ classifiers = [ "Development Status :: 4 - Beta",
 requires-python = ">=3.6"
 dependencies = [ "cython",
                  "numpy>=1.18.1",
+                 "bezier",
                  "mdtraj>=1.9.8",
                  "astunparse; python_version!='3.8'",
                  "astunparse<1.6.3; python_version=='3.8'",
@@ -36,7 +37,6 @@ dependencies = [ "cython",
                  "tqdm",
                  "ipywidgets",
                  "natsort",
-                 "bezier",
                  "mpl_chord_diagram>=0.3.2",
                  "docstring_parser",
                  ]