Merge pull request #60 from loucerac/develop

Develop

.github/workflows/docs_pages.yaml

@@ -1,42 +1,44 @@
 name: Docs2Pages
 on:
-  pull_request:
-    branches:
-      - master
+  workflow_run:
+    workflows: ["CI"]
+    types:
+      - completed
 permissions:
   contents: write
 jobs:
   build-docs:
     runs-on: ubuntu-latest
     steps:
-    - name: Checkout
-      uses: actions/checkout@master
-      with:
-        fetch-depth: 0
-    - uses: actions/setup-python@v2
-      with:
-        python-version: 3.8
-    - name: Install and configure Poetry
-      uses: snok/install-poetry@v1
-      with:
-        version: latest
-        virtualenvs-create: true
-        virtualenvs-in-project: true
-        installer-parallel: true
-    - name: Install package
-      run: poetry install
-    - name: Build documentation
-      run: |
-        mkdir gh-pages
-        touch gh-pages/.nojekyll
-        cd docs/
-        poetry run make html
-        cp -r build/* ../gh-pages/        
-        cd ../gh-pages/ 
-        cp -r html/* .
-        rm -rf html/
-    - name: Deploy documentation
-      uses: JamesIves/[email protected]
-      with:
-        branch: gh-pages
-        folder: gh-pages
+      - name: Checkout
+        uses: actions/checkout@master
+        with:
+          fetch-depth: 0
+      - uses: actions/setup-python@v2
+        with:
+          python-version: 3.8
+
+      - uses: pdm-project/setup-pdm@v3
+        with:
+          prerelease: false
+          enable-pep582: false
+          allow-python-prereleases: false
+
+      - name: Install package
+        run: pdm install
+
+      - name: Build documentation
+        run: |
+          mkdir gh-pages
+          touch gh-pages/.nojekyll
+          cd docs/
+          pdm run make html
+          cp -r build/* ../gh-pages/        
+          cd ../gh-pages/ 
+          cp -r html/* .
+          rm -rf html/
+      - name: Deploy documentation
+        uses: JamesIves/[email protected]
+        with:
+          branch: gh-pages
+          folder: gh-pages

.github/workflows/main.yml

@@ -6,9 +6,9 @@ name: CI
 on:
   # Triggers the workflow on push or pull request events but only for the master branch
   push:
-    branches: [ master, develop ]
+    branches: [master, develop]
   pull_request:
-    branches: [ master, develop ]
+    branches: [master, develop]
 
   # Allows you to run this workflow manually from the Actions tab
   workflow_dispatch:
@@ -21,29 +21,30 @@ jobs:
     timeout-minutes: 60
     strategy:
       matrix:
-        python-version: ['3.10']
+        python-version: ["3.10"]
 
     steps:
-    - uses: conda-incubator/setup-miniconda@v2
-      with:
-        auto-activate-base: true
-        activate-environment: ""
-
-    - uses: actions/checkout@v3
-
-    - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v4
-      with:
-        python-version: ${{ matrix.python-version }}
-
-    - name: Install and configure Poetry
-      uses: snok/install-poetry@v1
-      with:
-        version: latest
-        installer-parallel: true
-
-    - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip
-        python -m pip install nox nox-poetry
-    - run: nox
+      - uses: conda-incubator/setup-miniconda@v2
+        with:
+          auto-activate-base: true
+          activate-environment: ""
+
+      - uses: actions/checkout@v3
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Setup PDM
+        uses: pdm-project/setup-pdm@v3
+        with:
+          prerelease: false
+          enable-pep582: false
+          allow-python-prereleases: false
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install nox
+      - run: nox

.github/workflows/publish-to-test-pypi.yml

@@ -0,0 +1,52 @@
+name: Publish Python 🐍 distributions 📦 to PyPI and TestPyPI
+
+on:
+  push:
+    branches: [master]
+  pull_request:
+    branches: [master]
+
+jobs:
+  build-n-publish:
+    name: Build and publish Python 🐍 distributions 📦 to PyPI and TestPyPI
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v3
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.x"
+      - name: Setup PDM
+        uses: pdm-project/setup-pdm@v3
+        with:
+          prerelease: false
+          enable-pep582: false
+          allow-python-prereleases: false
+      # - name: Install pypa/build
+      #   run: >-
+      #     python3 -m
+      #     pip install
+      #     build
+      #     --user
+      # - name: Build a binary wheel and a source tarball
+      #   run: >-
+      #     python3 -m
+      #     build
+      #     --sdist
+      #     --wheel
+      #     --outdir dist/
+      #     .
+      - name: Build a binary wheel and a source tarball
+        run: >-
+          pdm build
+      - name: Publish distribution 📦 to Test PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          password: ${{ secrets.TEST_PYPI_API_TOKEN }}
+          repository-url: https://test.pypi.org/legacy/
+      - name: Publish distribution 📦 to PyPI
+        if: startsWith(github.ref, 'refs/tags')
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          password: ${{ secrets.PYPI_API_TOKEN }}

.gitignore

@@ -288,4 +288,5 @@ results_July2021_gpu
 scripts/automorf.ipynb
 debug.ipynb
 
-dask-worker-space/
+dask-worker-space/
+.pdm-python

README.md

@@ -2,34 +2,34 @@
 
 # Drug REpurposing using eXplainable Machine Learning and Mechanistic Models of signal transduction
 
-Repository for the `drexml` python package: (DRExM³L) Drug REpurposing using eXplainable Machine Learning and Mechanistic Models of signal transduction 
+Repository for the `drexml` python package: (DRExM³L) Drug REpurposing using eXplainable Machine Learning and Mechanistic Models of signal transduction
 
 ## Setup
 
 To install the `drexml` package use the following:
 
 ```
 conda create -n drexml python=3.10
-conda run -n drexml pip install git+https://github.com/loucerac/drexml.git@master
+conda activate drexml
+pip install drexml
 ```
 
-If a CUDA~11 compatible device is available use:
+If a CUDA~10.2/11.x (< 12) compatible device is available use:
 
 ```
 conda create -n drexml --override-channels -c "nvidia/label/cuda-11.8.0" -c conda-forge cuda cuda-nvcc cuda-toolkit gxx=11.2 python=3.10
-conda run -n drexml pip install git+https://github.com/loucerac/drexml.git@master
+conda activate drexml
+pip install --no-cache-dir --no-binary=shap drexml
 ```
 
 To install `drexml` in an existing environment, activate it and use:
 
 ```
-pip install git+https://github.com/loucerac/drexml.git@master
+pip install drexml
 ```
 
 Note that by default the `setup` will try to compile the `CUDA` modules, if not possible it will use the `CPU` modules.
 
-To install the development version use `@develop` instead of `@master`.
-
 ## Run
 
 To run the program for a disease map that uses circuits from the preprocessed `KEGG` pathways and the `KDT` standard list, construct an environment file (e.g. `disease.env`):
@@ -47,6 +47,7 @@ circuits=circuits.tsv.gz
 ```
 
 The `TSV` file `circuits.tsv` has the following format (tab delimited):
+
 ```
 index	in_disease
 P-hsa03320-37	0
@@ -69,8 +70,9 @@ P-hsa03320-28	1
 ```
 
 where:
-* `index`: Hipathia circuit id
-* `in_disease`: (boolean) True/1 if a given circuit is part of the disease
+
+- `index`: Hipathia circuit id
+- `in_disease`: (boolean) True/1 if a given circuit is part of the disease
 
 Note that in all cases you can restrict the circuits to the physiological list by setting `use_physio=true` in the `env` file.
 
@@ -81,27 +83,30 @@ drexml run --n-gpus 0 --n-cpus 10 $DISEASE_PATH
 ```
 
 where:
-* `--n-gpus` indicates the number of gpu devices to use in parallel (-1 -> all) (0 -> None)
-* `--n-cpus` indicates the number of cpu devices to use in parallel (-1 -> all) 8
-* `DISEASE_PATH` indicates the path to the disease env file (e.g. `/path/to/disease/folder/disease.env`)
+
+- `--n-gpus` indicates the number of gpu devices to use in parallel (-1 -> all) (0 -> None)
+- `--n-cpus` indicates the number of cpu devices to use in parallel (-1 -> all) 8
+- `DISEASE_PATH` indicates the path to the disease env file (e.g. `/path/to/disease/folder/disease.env`)
 
 Use the `--debug` option for testing that everything works using a few iterations.
 
 Note that the first time that the full program is run, it will take longer as it downloads the latest versions of each background dataset from Zenodo:
 
 https://doi.org/10.5281/zenodo.6020480
 
-
 ## Contribute to development
 
 The recommended setup is:
+
 - setup `pipx`
 - setup `miniforge`
-- use `pipx` to install `poetry`
-- use `pipx` to install `nox` and inject `nox-poetry` into `nox`
+- use `pipx` to install `pdm`
+- use `pipx` to inject pd-bump into `pdm`
+- use `pipx` to install `nox`
 - run `make`, if you want to use a CUDA enabled GPU, use `make gpu=1`
 
 ## Documentation
+
 The documentation can be found here:
 
 https://loucerac.github.io/drexml/

drexml/cli/cli.py

@@ -200,7 +200,11 @@ def run_cmd(ctx):
     cmd = build_cmd(ctx)
     # Unpythonic, update with dasks's LocalCudaCluster (currently unreliable).
     print(" ".join(cmd))
-    output = subprocess.run(cmd, capture_output=True, text=True, check=True)
+    try:
+        output = subprocess.run(cmd, capture_output=True, text=True, check=True)
+    except subprocess.CalledProcessError as err:  # pragma: no cover
+        click.echo("Ping stdout output:\n", err.output)
+
     if ctx["verbosity"]:
         click.echo(output.stderr)
         click.echo(output.stdout)

drexml/cli/stab_explainer.py

@@ -99,7 +99,6 @@
         print(f"{add=}")
 
         def runner(model, bkg, new, check_add, use_gpu):
-
             gpu_id = queue.get()
             if use_gpu:
                 explainer = shap.GPUTreeExplainer(model, bkg)

drexml/config.py

@@ -15,6 +15,7 @@
     "circuits_zenodo": False,
     "genes": None,
     "genes_zenodo": False,
+    "activity_normalizer": "false",
     "circuits_column": "in_disease",
     "genes_column": "drugbank_approved_targets",
     "GTEX_VERSION": "v8",

drexml/datasets.py

@@ -52,13 +52,12 @@ def fetch_file(key, env, version="latest"):
             try:
                 zenodo = Zenodo()
                 path = zenodo.download_latest(RECORD_ID, env[key], force=False)
-            except (ConnectTimeout) as err:
+            except ConnectTimeout as err:
                 print(err)
                 path = pathlib.Path.home().joinpath(
                     ".data", "zenodo", RECORD_ID, "20230612"
                 )
     else:
-
         path = env[key]
 
     print(key, path)