Merge pull request #614 from DeepRank/release_3.0.4_gcroci2

release: v3.0.4

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 3.0.3
+current_version = 3.0.4
 
 [comment]
 comment = The contents of this file cannot be merged with that of setup.cfg until https://github.com/c4urself/bump2version/issues/185 is resolved

.github/workflows/linting.yml

@@ -30,7 +30,7 @@ on:
 jobs:
   build:
     if: github.event.pull_request.draft == false
-    name: Linting build
+    name: Linting
     runs-on: ${{ matrix.os }}
 
     strategy:
@@ -46,11 +46,17 @@ jobs:
 
     steps:
       - uses: actions/checkout@v3
-      - uses: ./.github/actions/install-python-and-package
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v3
         with:
           python-version: ${{ matrix.python-version }}
-          extras-require: test
-      - name: Check style against standards using ruff
+      - name: Python info
+        shell: bash -l {0}
+        run: |
+          which python3
+          python3 --version
+      - name: Check linting and formatting using ruff
         run: |
-          ruff check
-          ruff format --check
+          python3 -m pip install ruff
+          ruff check || (echo "Please ensure you have the latest version of ruff (`ruff -V`) installed locally." && (exit 1))
+          ruff format --check || (echo "Please ensure you have the latest version of ruff (`ruff -V`) installed locally." && (exit 1))

CITATION.cff

@@ -86,4 +86,4 @@ preferred-citation:
   volume: 9
 title: "DeepRank2: Mining 3D Protein Structures with Geometric Deep
   Learning"
-version: "3.0.3"
+version: "3.0.4"

Dockerfile

@@ -14,6 +14,8 @@ RUN \
   apt install -y gcc && \
   ## Create the environment and install the dependencies
   mamba env create -f /home/deeprank2/deeprank2-docker.yml && \
+  ## Activate the environment and install pip packages
+  /opt/conda/bin/conda run -n deeprank2 pip install -r /home/deeprank2/requirements-docker.txt && \
   ## Activate the environment automatically when entering the container
   echo "source activate deeprank2" >~/.bashrc && \
   # Get the data for running the tutorials

deeprank2/__init__.py

@@ -1 +1 @@
-__version__ = "3.0.3"
+__version__ = "3.0.4"

deeprank2/features/secondary_structure.py

@@ -103,7 +103,7 @@ def _get_secstructure(pdb_path: str) -> dict:
 
     try:
         dssp = DSSP(model, pdb_path, dssp="mkdssp")
-    except Exception as e:  # noqa: BLE001, namely: # improperly formatted pdb files raise: `Exception: DSSP failed to produce an output`
+    except Exception as e:
         pdb_format_link = "https://www.wwpdb.org/documentation/file-format-content/format33/sect1.html#Order"
         msg = (
             f"DSSP has raised the following exception: {e}.\n\t"

env/deeprank2-docker.yml

@@ -41,5 +41,3 @@ dependencies:
   - ruff>=0.3.0
   - dill>=0.3.8
   - pyarrow>=15.0.0
-  - pip:
-      - --requirement requirements-docker.txt

env/deeprank2.yml

@@ -7,13 +7,9 @@ channels:
   - conda-forge
   - sbl
 dependencies:
-  - python==3.10
-  - pip>=23.3
-  - notebook>=7.0.6
   - sbl::libcifpp>=5.1.0
   - sbl::dssp>=4.2.2.1
   - msms>=2.6.1
-  - markov_clustering>=0.0.6
   - pytorch=2.1.1
   - torchvision>=0.16.1
   - torchaudio>=2.1.1
@@ -23,21 +19,3 @@ dependencies:
   - pytorch-sparse>=0.6.18
   - pytorch-cluster>=1.6.3
   - pytorch-spline-conv>=1.2.2
-  - tables>=3.8.0
-  - numpy>=1.21.5
-  - scipy>=1.13.1
-  - h5py>=3.6.0
-  - networkx>=2.6.3
-  - matplotlib>=3.5.1
-  - scikit-learn>=1.0.2
-  - chart-studio>=1.1.0
-  - biopython>=1.81
-  - pdb2sql>=0.5.1
-  - python-louvain>=0.16
-  - tqdm>=4.63.0
-  - freesasa>=2.1.0
-  - tensorboard>=0.9.0
-  - protobuf>=3.20.1
-  - ruff>=0.3.0
-  - dill>=0.3.8
-  - pyarrow>=15.0.0

env/requirements-docker.txt

@@ -1 +1 @@
-deeprank2==3.0.3
+deeprank2==3.0.4

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "deeprank2"
-version = "3.0.3"
+version = "3.0.4"
 description = "DeepRank2 is an open-source deep learning framework for data mining of protein-protein interfaces or single-residue missense variants."
 readme = "README.md"
 requires-python = ">=3.10"
@@ -34,6 +34,27 @@ classifiers = [
     "Programming Language :: Python :: 3",
     "Programming Language :: Python :: 3.10",
 ]
+dependencies = [
+    "notebook >= 7.0.6",
+    "markov-clustering >= 0.0.6.dev0",
+    "tensorboard>=0.9.0",
+    "protobuf >= 3.20.1",
+    "dill >= 0.3.8",
+    "pyarrow >= 15.0.0",
+    "tables >= 3.8.0",
+    "numpy >= 1.25, < 2.0",
+    "scipy >= 1.13.1",
+    "h5py >= 3.6.0",
+    "networkx >= 2.6.3",
+    "matplotlib >= 3.5.1",
+    "scikit-learn >= 1.0.2",
+    "chart-studio >= 1.1.0",
+    "pdb2sql >= 0.5.1",
+    "python-louvain >= 0.16",
+    "tqdm >= 4.63.0",
+    "freesasa >= 2.1.0",
+    "biopython >= 1.81"
+    ]
 
 [project.optional-dependencies]
 # development dependency groups
@@ -45,6 +66,7 @@ test = [
     "pytest-cov",
     "pytest-runner",
     "coveralls",
+    "ruff>=0.3.0"
 ]
 publishing = ["build", "twine", "wheel"]
 notebooks = ["nbmake"]