build: improve installation making use of pyproject.toml file only and setuptools

.bumpversion.cfg

@@ -8,7 +8,7 @@ comment = The contents of this file cannot be merged with that of setup.cfg unti
 search = __version__ = "{current_version}"
 replace = __version__ = "{new_version}"
 
-[bumpversion:file:setup.cfg]
+[bumpversion:file:pyproject.toml]
 search = version = {current_version}
 replace = version = {new_version}
 

.github/actions/install-python-and-package/action.yml

@@ -6,8 +6,8 @@ inputs:
 
   python-version:
     required: false
-    description: "The Python version to use. Specify major and minor version, e.g. '3.9'."
-    default: "3.9"
+    description: "The Python version to use. Specify major and minor version, e.g. '3.10'."
+    default: "3.10"
 
   extras-require:
     required: false
@@ -24,12 +24,6 @@ runs:
       with:
           access_token: ${{ github.token }}
     - uses: actions/checkout@v3
-    - uses: actions/setup-python@v4
-      with:
-        python-version: ${{ inputs.python-version }}
-        cache: 'pip'
-        cache-dependency-path: setup.cfg
-
     - name: Setup conda
       uses: s-weigand/setup-conda@v1
       with:
@@ -38,29 +32,70 @@ runs:
         conda-channels: anaconda
     - run: conda --version
       shell: bash {0}
-    - run: which python
-      shell: bash {0}
-
-    - name: Upgrade pip and install dependencies
+    - name: Python info
+      shell: bash -e {0}
+      run: |
+        which python3
+        python3 --version
+    - name: Install dependencies on Linux
       shell: bash {0}
       env:
         CMAKE_INSTALL_PREFIX: .local
+      if: runner.os == 'Linux'
       run: |
-        python3 -m pip install --upgrade pip setuptools wheel
-        # Install dssp
+        # Install dependencies not handled by setuptools 
+        ## DSSP
         sudo apt-get install -y dssp
-        # Only way to install msms is through conda
+        ## MSMS
         conda install -c bioconda msms
-        # Safest way to install PyTorch and PyTorch Geometric is through conda
-        conda install pytorch==2.0.0 torchvision=0.15.0 torchaudio=2.0.0 cpuonly -c pytorch
+        ## PyTorch, PyG, PyG adds
+        ### Installing for CPU only on the CI
+        conda install pytorch torchvision torchaudio cpuonly -c pytorch
         conda install pyg -c pyg
-        # Install optional pyg dependencies
-        python3 -m pip install pyg_lib torch_scatter torch_sparse torch_cluster torch_spline_conv -f https://data.pyg.org/whl/torch-$(python3 -c "import torch; print(torch.__version__)")+cpu.html
-        # In the future, release h5xplorer on PyPI
-        pip install git+https://github.com/DeepRank/h5xplorer.git@master
-
-    - name: Install the package
+        pip install torch_scatter torch_sparse torch_cluster torch_spline_conv -f https://data.pyg.org/whl/torch-$(python3 -c "import torch; print(torch.__version__)")+cpu.html
+    - name: Install dependencies on MacOS
       shell: bash {0}
-      run: python3 -m pip install .[${{ inputs.extras-require }}]
       env:
-        CONDA_PREFIX: /usr/share/miniconda
+        CMAKE_INSTALL_PREFIX: .local
+      if: runner.os == 'macOS'
+      run: |
+        # Install dependencies not handled by setuptools 
+        ## DSSP
+        git clone https://github.com/PDB-REDO/libcifpp.git --recurse-submodules
+        cd libcifpp
+        cmake -S . -B build -DCMAKE_INSTALL_PREFIX=$HOME/.local -DCMAKE_BUILD_TYPE=Release
+        cmake --build build
+        cmake --install build
+        #######
+        git clone https://github.com/mhekkel/libmcfp.git
+        cd libmcfp
+        mkdir build
+        cd build
+        cmake ..
+        cmake --build .
+        cmake --install .
+        #######
+        git clone https://github.com/PDB-REDO/dssp.git
+        cd dssp
+        mkdir build
+        cmake -S . -B build -DCMAKE_BUILD_TYPE=Release
+        cmake --build build
+        cmake --install build
+        ## MSMS
+        cd /tmp/
+        wget http://mgltools.scripps.edu/downloads/tars/releases/MSMSRELEASE/REL2.6.1/msms_i86Linux2_2.6.1.tar.gz
+        sudo mkdir /usr/local/lib/msms
+        cd /usr/local/lib/msms
+        sudo tar zxvf /tmp/msms_i86Linux2_2.6.1.tar.gz
+        sudo ln -s /usr/local/lib/msms/msms.i86Linux2.2.6.1 /usr/local/bin/msms
+        sudo ln -s /usr/local/lib/msms/pdb_to_xyzr* /usr/local/bin
+        ## PyTorch, PyG, PyG adds
+        ### Installing for CPU only on the CI
+        conda install pytorch torchvision torchaudio cpuonly -c pytorch
+        pip install torch_geometric
+        pip install torch_scatter torch_sparse torch_cluster torch_spline_conv -f https://data.pyg.org/whl/torch-$(python3 -c "import torch; print(torch.__version__)")+cpu.html
+        # PyTables via conda only for MacOS
+        conda install pytables
+    - name: Install the package
+      shell: bash {0}
+      run: pip install .'[${{ inputs.extras-require }}]'

.github/workflows/build.yml

@@ -37,15 +37,15 @@ jobs:
       fail-fast: false
       matrix:
         os: ['ubuntu-latest']
-        python-version: ['3.9', '3.10']
+        python-version: ['3.10', '3.11']
 
     steps:
       - uses: actions/checkout@v3
       - uses: ./.github/actions/install-python-and-package
+        with:
+          python-version: ${{ matrix.python-version }}
+          extras-require: test, publishing
       - name: Run unit tests
-        env:
-          CONDA_PREFIX: /usr/share/miniconda
-        run: |
-          pytest -v
+        run: pytest -v
       - name: Verify that we can build the package
-        run: python3 setup.py sdist bdist_wheel
+        run: python3 -m build

.github/workflows/coveralls.yml

@@ -37,16 +37,19 @@ jobs:
       fail-fast: false
       matrix:
         os: ["ubuntu-latest"]
-        python-version: [3.9]
+        python-version: ['3.10']
 
     steps:
       - uses: actions/checkout@v3
       - uses: ./.github/actions/install-python-and-package
+        with:
+          python-version: ${{ matrix.python-version }}
+          extras-require: test
       - name: Run unit tests with coverage
         run: pytest --cov --cov-append --cov-report xml --cov-report term --cov-report html
       - name: Coveralls
         env:
           GITHUB_TOKEN: ${{ secrets.github_token }}
           COVERALLS_FLAG_NAME: python-${{ matrix.os }}
         run: |
-          coveralls --service=github
+          coveralls --service=github

.github/workflows/linting.yml

@@ -37,10 +37,13 @@ jobs:
       fail-fast: false
       matrix:
         os: ["ubuntu-latest"]
-        python-version: [3.9]
+        python-version: ['3.10']
 
     steps:
       - uses: actions/checkout@v3
       - uses: ./.github/actions/install-python-and-package
+        with:
+          python-version: ${{ matrix.python-version }}
+          extras-require: test
       - name: Check style against standards using prospector
-        run: prospector --die-on-tool-error
+        run: prospector --die-on-tool-error

.github/workflows/release.yml

@@ -15,12 +15,13 @@ jobs:
       fail-fast: false
       matrix:
         os: ['ubuntu-latest']
-        python-version: [3.9]
+        python-version: ['3.10']
 
     steps:
       - uses: actions/checkout@v3
       - uses: ./.github/actions/install-python-and-package
         with:
+          python-version: ${{ matrix.python-version }}
           extras-require: publishing
       - name: Build wheel and source distribution
         run: python -m build

.gitignore

@@ -41,4 +41,6 @@ docs/apidocs
 
 #other
 *_.ipynb
-Untitled*
+Untitled*
+data_raw/
+data_processed/

README.md

@@ -5,10 +5,10 @@
 | **fairness** |  [![fair-software.eu](https://img.shields.io/badge/fair--software.eu-%E2%97%8F%20%20%E2%97%8F%20%20%E2%97%8F%20%20%E2%97%8F%20%20%E2%97%8F-green)](https://fair-software.eu) [![CII Best Practices](https://bestpractices.coreinfrastructure.org/projects/6403/badge)](https://bestpractices.coreinfrastructure.org/projects/6403) |
 | **package** |  [![PyPI version](https://badge.fury.io/py/deeprank2.svg)](https://badge.fury.io/py/deeprank2) [![Codacy Badge](https://api.codacy.com/project/badge/Grade/f3f98b2d1883493ead50e3acaa23f2cc)](https://app.codacy.com/gh/DeepRank/deeprank2?utm_source=github.com&utm_medium=referral&utm_content=DeepRank/deeprank2&utm_campaign=Badge_Grade) |
 | **docs** | [![Documentation Status](https://readthedocs.org/projects/deeprank2/badge/?version=latest)](https://deeprank2.readthedocs.io/en/latest/?badge=latest) [![DOI](https://zenodo.org/badge/450496579.svg)](https://zenodo.org/badge/latestdoi/450496579) |
-| **tests** | [![Build Status](https://github.com/DeepRank/deeprank2/actions/workflows/build.yml/badge.svg)](https://github.com/DeepRank/deeprank2/actions) ![Linting status](https://github.com/DeepRank/deeprank2/actions/workflows/linting.yml/badge.svg?branch=main) [![Coverage Status](https://coveralls.io/repos/github/DeepRank/deeprank2/badge.svg?branch=main)](https://coveralls.io/github/DeepRank/deeprank2?branch=main) |
+| **tests** | [![Build Status](https://github.com/DeepRank/deeprank2/actions/workflows/build.yml/badge.svg)](https://github.com/DeepRank/deeprank2/actions) ![Linting status](https://github.com/DeepRank/deeprank2/actions/workflows/linting.yml/badge.svg?branch=main) [![Coverage Status](https://coveralls.io/repos/github/DeepRank/deeprank2/badge.svg?branch=main)](https://coveralls.io/github/DeepRank/deeprank2?branch=main) ![Python](https://img.shields.io/badge/python-3.10-blue.svg)  ![Python](https://img.shields.io/badge/python-3.11-blue.svg) |
+| **running on** | ![Ubuntu](https://img.shields.io/badge/Ubuntu-E95420?style=for-the-badge&logo=ubuntu&logoColor=white) |
 | **license** |  [![License](https://img.shields.io/badge/License-Apache_2.0-blue.svg)](https://opensource.org/license/apache-2-0/)  |
 
-
 ## Overview
 
 ![alt-text](./deeprank2.png)
@@ -46,35 +46,22 @@ DeepRank2 extensive documentation can be found [here](https://deeprank2.rtfd.io/
       - [GraphDataset](#graphdataset)
       - [GridDataset](#griddataset)
     - [Training](#training)
-  - [h5x support](#h5x-support)
   - [Package development](#package-development)
 
 ## Installation
 
 ### Dependencies
 
-Before installing deeprank2 you need to install some dependencies. We advise to use a [conda environment](https://conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html) with Python >= 3.9 installed.
-
-* [msms](https://ssbio.readthedocs.io/en/latest/instructions/msms.html): `conda install -c bioconda msms`. *For MacOS with M1 chip users*: you can follow [these instructions](https://ssbio.readthedocs.io/en/latest/instructions/msms.html).
-* [PyTorch](https://pytorch.org/):
-  * CPU only: `conda install pytorch==2.0.0 torchvision==0.15.0 torchaudio==2.0.0 cpuonly -c pytorch`
-  * if using GPU: `conda install pytorch==2.0.0 torchvision==0.15.0 torchaudio==2.0.0 pytorch-cuda=11.7 -c pytorch -c nvidia`
-* [pytorch-geometric](https://pytorch-geometric.readthedocs.io/en/latest/notes/installation.html): `conda install pyg -c pyg`
-* [Dependencies for pytorch geometric from wheels](https://pytorch-geometric.readthedocs.io/en/latest/install/installation.html#installation-from-wheels): `pip install pyg_lib torch_scatter torch_sparse torch_cluster torch_spline_conv -f https://data.pyg.org/whl/torch-${TORCH}+${CUDA}.html`.
-  - Here, `${TORCH}` and `${CUDA}` should be replaced by the pytorch and CUDA versions installed. You can find these using:
-    - `python -c "import torch; print(torch.__version__)"` and
-    - `python -c "import torch; print(torch.version.cuda)"`
-      - if this returns `None`, use `cpu` instead
-  - For example: `pip install pyg_lib torch_scatter torch_sparse torch_cluster torch_spline_conv -f https://data.pyg.org/whl/torch-2.0.0+cpu.html`
-* Check if [DSSP 4](https://swift.cmbi.umcn.nl/gv/dssp/) is installed: `dssp --version`
-  * if this gives an error or shows a version lower than 4:
-    * on ubuntu 22.04 or newer: `sudo apt-get install dssp`.
-      * If the package cannot be located, first run `sudo apt-get update`.
-    * on older versions of ubuntu or on mac or lacking sudo priviliges: install from [here](https://github.com/pdb-redo/dssp), following the instructions listed.
-* Check if gcc is installed: `gcc --version`.
-  * if this gives an error, run `sudo apt-get install gcc`.
-
-* For MacOS with M1 chip (otherwise ignore this): `conda install pytables`
+Before installing deeprank2 you need to install some dependencies. We advise to use a [conda environment](https://conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html) with Python >= 3.9 installed. Follow the official documentation linked below:
+
+*  [MSMS](https://ssbio.readthedocs.io/en/latest/instructions/msms.html)
+  *  [Here](https://ssbio.readthedocs.io/en/latest/instructions/msms.html) for MacOS with M1 chip users
+*  [PyTorch](https://pytorch.org/get-started/locally/)
+  *  We support torch's CPU library as well as CUDA
+*  [PyG](https://pytorch-geometric.readthedocs.io/en/latest/install/installation.html) and its optional dependencies: `torch_scatter`, `torch_sparse`, `torch_cluster`, `torch_spline_conv`
+*  [DSSP 4](https://swift.cmbi.umcn.nl/gv/dssp/)
+*  [GCC](https://gcc.gnu.org/install/)
+*  For MacOS with M1 chip users only install [the conda version of PyTables](https://www.pytables.org/usersguide/installation.html)
 
 ### Deeprank2 Package
 
@@ -84,12 +71,12 @@ Once the dependencies are installed, you can install the latest stable release o
 pip install deeprank2
 ```
 
-Alternatively, get all the new developments by cloning the repo and installing the code with
+Alternatively, get all the new developments by cloning the repo and installing the editable version of the package with
 
 ```bash
 git clone https://github.com/DeepRank/deeprank2
 cd deeprank2
-pip install -e ./
+pip install -e .
 ```
 
 ### Test installation
@@ -319,10 +306,6 @@ trainer.test()
 
 ```
 
-## h5x support
-
-After installing  `h5xplorer`  (https://github.com/DeepRank/h5xplorer), you can execute the python file `deeprank2/h5x/h5x.py` to explorer the connection graph used by deeprank2. The context menu (right click on the name of the structure) allows to automatically plot the graphs using `plotly`.
-
 ## Package development
 
 - Branching