Merge pull request #52 from loucerac/develop

Develop

.github/workflows/docs_pages.yaml

@@ -16,8 +16,14 @@ jobs:
     - uses: actions/setup-python@v2
       with:
         python-version: 3.8
-    - uses: abatilo/[email protected]
-    - name: install
+    - 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: |

.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 ]
+    branches: [ master, develop ]
   pull_request:
-    branches: [ master ]
+    branches: [ master, develop ]
 
   # Allows you to run this workflow manually from the Actions tab
   workflow_dispatch:
@@ -18,27 +18,32 @@ on:
 jobs:
   build:
     runs-on: ubuntu-latest
-    timeout-minutes: 30
+    timeout-minutes: 60
     strategy:
       matrix:
-        python-version: ['3.8', '3.9', '3.10']
+        python-version: ['3.10']
 
     steps:
-    - uses: actions/checkout@v1
+    - 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@v2
+      uses: actions/setup-python@v4
       with:
         python-version: ${{ matrix.python-version }}
+
     - name: Install and configure Poetry
       uses: snok/install-poetry@v1
       with:
-        version: 1.1.10
-        virtualenvs-create: true
-        virtualenvs-in-project: true
+        version: latest
         installer-parallel: true
+
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        python -m pip install tox tox-gh-actions tox-poetry
-    - name: Test with tox
-      run: tox
+        python -m pip install nox nox-poetry
+    - run: nox

.gitignore

@@ -143,6 +143,7 @@ coverage.xml
 *.cover
 .hypothesis/
 .pytest_cache/
+.nox/
 
 # Translations
 *.mo

.pylintrc

@@ -438,7 +438,9 @@ valid-metaclass-classmethod-first-arg=cls
 [DESIGN]
 
 # Maximum number of arguments for function / method.
-max-args=5
+max-args=10
+max-function-args=10
+
 
 # Maximum number of attributes for a class (see R0902).
 max-attributes=7
@@ -506,4 +508,5 @@ known-third-party=enchant
 # Exceptions that will emit a warning when being caught. Defaults to
 # "BaseException, Exception".
 overgeneral-exceptions=BaseException,
-                       Exception
+                       Exception
+

.vscode/settings.json

@@ -9,16 +9,19 @@
     "files.watcherExclude": {
         "**/venvs": true,
         "**/.venv": true,
+        "**/__pycache__": true,
         "**/data": true
     },
     "files.exclude": {
         "**/venvs": true,
         "**/.venv": true,
+        "**/__pycache__": true,
         "**/data": true
     },
     "search.exclude": {
         "**/venvs": true,
         "**/.venv": true,
+        "**/__pycache__": true,
         "**/data": true
     },
     "python.testing.pytestArgs": [

LICENSE.txt

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) [year] [fullname]
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

README.md

@@ -1,18 +1,35 @@
 [![DOI](https://zenodo.org/badge/362395439.svg)](https://zenodo.org/badge/latestdoi/362395439)
 
-# Drug REpurposing using Mechanistic Models of signal transduction and -eXplainable Machine Learning
+# Drug REpurposing using eXplainable Machine Learning and Mechanistic Models of signal transduction
 
-Repository for the `drexml` python package: (DRExM³L) Drug REpurposing using Mechanistic Models of signal transduction and eXplainable Machine Learning 
+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=3.8
-conda run -n drexml pip install git+ssh://git@github.com:loucerac/drexml.git
+conda create -n drexml python=3.10
+conda run -n drexml pip install git+https://github.com/loucerac/drexml.git@master
 ```
 
+If a CUDA~11 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
+```
+
+To install `drexml` in an existing environment, activate it and use:
+
+```
+pip install git+https://github.com/loucerac/drexml.git@master
+```
+
+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`) using the following template:
@@ -26,26 +43,26 @@ genes=$default$
 genes_column=approved_targets
 ```
 
-Where `circuits.tsv` has the following format (tab delimited):
+The `TSV` file `circuits.tsv` has the following format (tab delimited):
 ```
 index	in_disease
-P-hsa03320-37	False
-P-hsa03320-61	False
-P-hsa03320-46	False
-P-hsa03320-57	False
-P-hsa03320-64	False
-P-hsa03320-47	False
-P-hsa03320-65	False
-P-hsa03320-55	False
-P-hsa03320-56	False
-P-hsa03320-33	False
-P-hsa03320-58	False
-P-hsa03320-59	False
-P-hsa03320-63	False
-P-hsa03320-44	False
-P-hsa03320-36	False
-P-hsa03320-30	False
-P-hsa03320-28	True
+P-hsa03320-37	0
+P-hsa03320-61	0
+P-hsa03320-46	0
+P-hsa03320-57	0
+P-hsa03320-64	0
+P-hsa03320-47	0
+P-hsa03320-65	0
+P-hsa03320-55	0
+P-hsa03320-56	0
+P-hsa03320-33	0
+P-hsa03320-58	0
+P-hsa03320-59	0
+P-hsa03320-63	0
+P-hsa03320-44	0
+P-hsa03320-36	0
+P-hsa03320-30	0
+P-hsa03320-28	1
 ```
 
 where:
@@ -67,6 +84,15 @@ Note that the first time that the full program is run, it will take longer as it
 
 https://doi.org/10.5281/zenodo.6020480
 
+## Contribute to development
+
+The recommended setup is:
+- setup `pipx`
+- setup `miniconda`
+- use `pipx` to install `poetry`
+- use `pipx` to install `nox` and inject `nox-poetry` into `nox`
+- run `make`, if you want to use a CUDA enabled GPU, use `make gpu=1`
+
 ## Documentation
 The documentation can be found here:
 

docs/source/api_reference.rst

@@ -26,4 +26,9 @@ explain
 utils
 ----------
 .. automodule:: drexml.utils
+   :members:
+
+plotting
+----------
+.. automodule:: drexml.plotting
    :members:

drexml/cli/cli.py

@@ -14,11 +14,29 @@
 import shutil
 import subprocess
 import sys
+import warnings
 
 import click
 import joblib
+from numba.core.errors import NumbaDeprecationWarning, NumbaPendingDeprecationWarning
 
-from drexml.utils import get_data, get_number_cuda_devices, get_out_path, get_version
+with warnings.catch_warnings():
+    warnings.filterwarnings(
+        "ignore", module="shap", message="IPython could not be loaded!"
+    )
+    warnings.filterwarnings("ignore", module="shap", category=NumbaDeprecationWarning)
+    warnings.filterwarnings(
+        "ignore", module="shap", category=NumbaPendingDeprecationWarning
+    )
+
+from drexml.plotting import plot_metrics
+from drexml.utils import (
+    get_data,
+    get_number_cuda_devices,
+    get_out_path,
+    get_version,
+    rename_results,
+)
 
 FNAME_DICT = {
     "train": "stab_trainer.py",
@@ -80,6 +98,25 @@
 ]
 
 
+_check_add_option = [
+    click.option(
+        "--add/--no-add",
+        is_flag=True,
+        default=True,
+        help="Check the additivity when computing the SHAP values.",
+    )
+]
+
+_verb_option = [
+    click.option(
+        "--verbosity/--no-verbosity",
+        is_flag=True,
+        default=False,
+        help="Verbosity level.",
+    )
+]
+
+
 def copy_files(ctx, fnames):
     """Copy files from tmp to ml folder."""
     for fname in fnames:
@@ -148,6 +185,7 @@ def build_cmd(ctx):
         str(int(ctx["n_gpus"])),
         str(ctx["n_cpus"]),
         str(int(ctx["debug"])),
+        str(int(ctx["add"])),
         ctx["mode"],
     ]
 
@@ -160,19 +198,21 @@ def run_cmd(ctx):
     # Unpythonic, update with dasks's LocalCudaCluster (currently unreliable).
     print(" ".join(cmd))
     output = subprocess.run(cmd, capture_output=True, text=True, check=True)
-    click.echo(output.stderr)
-    click.echo(output.stdout)
+    if ctx["verbosity"]:
+        click.echo(output.stderr)
+        click.echo(output.stdout)
 
 
 @click.group()
 @click.version_option(get_version())
 def main():
     """drexml CLI entry point."""
-    print(f"running drexml orchestrate v {get_version()}")
+    print(f"running drexml v{get_version()}")
 
 
 @main.command()
 @add_options(_debug_option)
+@add_options(_verb_option)
 @click.argument("disease-path", type=click.Path(exists=True))
 @click.version_option(get_version())
 def orchestrate(**kwargs):
@@ -193,6 +233,7 @@ def orchestrate(**kwargs):
     type=click.Choice(["train", "explain", "score"], case_sensitive=False),
 )
 @add_options(_debug_option)
+@add_options(_verb_option)
 @add_options(_n_iters_option)
 @add_options(_n_gpus_option)
 @add_options(_n_cpus_option)
@@ -223,6 +264,8 @@ def stability(**kwargs):
 
 @main.command()
 @add_options(_debug_option)
+@add_options(_verb_option)
+@add_options(_check_add_option)
 @add_options(_n_iters_option)
 @add_options(_n_gpus_option)
 @add_options(_n_cpus_option)
@@ -240,6 +283,8 @@ def explain(**kwargs):
 
 @main.command()
 @add_options(_debug_option)
+@add_options(_verb_option)
+@add_options(_check_add_option)
 @add_options(_n_iters_option)
 @add_options(_n_gpus_option)
 @add_options(_n_cpus_option)
@@ -257,5 +302,25 @@ def run(ctx, **kwargs):
     ctx.forward(explain)
 
 
+@main.command()
+@click.argument("stab-path", type=click.Path(exists=True))
+@click.version_option(get_version())
+@click.pass_context
+def plot(ctx, stab_path):
+    """Plot the stability results"""
+
+    plot_metrics(stab_path)
+
+
+@main.command()
+@click.argument("results-folder", type=click.Path(exists=True))
+@click.version_option(get_version())
+@click.pass_context
+def rename(ctx, results_folder):
+    """Plot the stability results"""
+
+    rename_results(results_folder)
+
+
 if __name__ == "__main__":
     main()