Clean/versions

.github/workflows/lint_and_test.yaml

@@ -5,6 +5,7 @@ on:
     branches:
       - main
       - dev
+      - staging
       - production
     paths:
       - 'src/**'
@@ -14,6 +15,7 @@ on:
     branches:
       - main
       - dev
+      - staging
       - production
     paths:
       - 'src/**'
@@ -49,23 +51,18 @@ jobs:
         run: pip install ruff==${{ env.RUFF_VERSION }}
       - name: ruff format (check code formatting)
         run: ruff format --diff
-      # - name: ruff check (lint code base)
-      #   run: ruff check
+      - name: ruff check (lint code base)
+        run: ruff check src tests
 
   test_digs:
     name: pytest (run tests)
     runs-on: [jojo]
     timeout-minutes: 30
     needs: lint
-    # ... only run on non-draft PRs to `main` to avoid unnecessary CI runs
-    # ... and only run on changed files in the `atomworks`, `tests`, or `scripts` directories
-    if: |
-      (github.event_name == 'pull_request' && !github.event.pull_request.draft) ||
-      (github.event_name == 'pull_request_target' && github.event.action == 'ready_for_review')
+    if: github.event_name == 'workflow_dispatch'
     steps:
       - uses: actions/checkout@v4
       - name: Run tests
-        timeout-minutes: 30
         run: |
           export N_CPU=8
           srun --chdir=$PWD -p cpu -c $N_CPU -t 00:30:00 --mem=32G bash ./.github/ci/run_tests.sh
@@ -110,7 +107,7 @@ jobs:
         run: |
           atomworks setup tests
 
-      - name: Run pytest with multiple cores
+      - name: Run pytest
         run: |
           export OPENBLAS_NUM_THREADS=1
           export OMP_NUM_THREADS=1

pyproject.toml

@@ -27,30 +27,27 @@ dependencies = [
     "cytoolz>=0.12.3,<1", # Cython-optimized tools for itertools and functional programming
     "tqdm>=4.65.0,<5", # Fast, extensible progress bar for loops and more
     # ... CLI & config management
-    "fire>=0.6.0,<1", # Argument parsing (legacy)
     "typer>=0.12.5,<1", # Modern CLI framework
     # ... linear algebra, maths & ml
     "numpy>=1.25.0,<2",  # TODO: Enable numpy 2.x
     "scipy>=1.13.1,<2",
     # ... data tools
     "pandas>=2.2,<2.3", # Data manipulation and analysis  # TODO: Test upper bound
     "pyarrow==17.0.0", # Columnar data format for efficient data storage and processing  # TODO: Test later versions
-    "fastparquet==2024.5.0", # Fast Parquet file format implementation # TODO: Test if still needed
     # ... bioinformatics
     "py3Dmol>=2.2.1,<3", # Python wrapper for 3Dmol.js
     "pymol-remote>=0.0.5", # Remote access to PyMOL from Python (has no dependencies)
-    "biotite==1.3.0", # Biotite is a Python library for bioinformatics  # TODO: Test newer versions
-    "hydride==1.2.3", # Biotite-supported tool for hydrogen addition
+    "biotite>=1.3.0,<2", # Biotite is a Python library for bioinformatics  # TODO: Test newer versions
+    "hydride>=1.2.3,<2", # Biotite-supported tool for hydrogen addition
     # ... small molecule libraries
-    "rdkit>=2024.3.5",
-
+    "rdkit>=2024.3.5,<2025.9",
 ]
 
 [project.optional-dependencies]
 ml = [
     # atomworks-ml dependencies
-    "torch==2.7.0",
-    "einops==0.7.0",
+    "torch>=2.2.0,<2.8",
+    "einops>=0.7.0,<1",
 ]
 
 openbabel = [
@@ -61,10 +58,6 @@ openbabel = [
 dev = [
     # Linters & formatters
     "ruff==0.8.3",
-    "pre-commit==3.7.1",
-    # Debugger/interactive
-    "debugpy>=1.8.5,<2",
-    "ipykernel>=6.29.4,<7",
     # Testing tools
     "pytest>=8.2.0,<9", # testing framework
     "pytest-testmon>=2.1.1,<3", # run only tests related to changed code