fix: expose train script in pypi (#20)

* refactor: only use pip, remove conda

* ci: add workflow to push to pypi on release

* fix: make train script available when installed using pip

* fix: bump ci python to 3.8

* fix: macos-14 does not have python version <3.10 so use macos13

* fix: bump python to 3.10, remove loader.py, train_baseline.py

* deps: remove tensorflow and deepchem deps

* fix: python version shall be string

* fix: test macos-13 again

* ci: run ci

* chore: bump version to 1.0.0

.github/workflows/build.yml

@@ -13,7 +13,7 @@ jobs:
           - os: ubuntu-20.04
             pip_cache_path: ~/.cache/pip
             experimental: false
-          - os: macos-latest
+          - os: macos-13
             pip_cache_path: ~/Library/Caches/pip
             experimental: false
     defaults:
@@ -28,39 +28,25 @@ jobs:
       - name: Checkout and setup python
         uses: actions/setup-python@v2
         with:
-          python-version: 3.6
+          python-version: '3.10'
           architecture: 'x64'
 
-      - name: Cache conda
-        uses: actions/cache@v2
-        with:
-          path: ~/conda_pkgs_dir  # from: conda-incubator/setup-miniconda@v2
-          key: ${{ runner.os }}-conda-${{ env.CACHE_NUMBER }}-${{
-            hashFiles('conda.yml') }}
-
       - name: Cache pip
         uses: actions/cache@v2
         with:
           path: ${{ matrix.pip_cache_path }}
           key: ${{ runner.os }}-pip--${{ env.CACHE_NUMBER }}-${{
             hashFiles('requirements.txt') }}
 
-      - name: Conda environment setup
-        uses: conda-incubator/setup-miniconda@v2
-        with:
-          activate-environment: toxsmi
-          environment-file: conda.yml
-          auto-activate-base: false
-          use-only-tar-bz2: true  # This needs to be set for proper caching
-          auto-update-conda: true  # Required for windows for `use-only-tar-bz2`
-
       - name: Install dependencies and test code 
         run: |
           pip3 install --no-cache-dir -r requirements.txt
           pip3 install --no-deps .
           python3 -c "import toxsmi"
           python3 scripts/train_baselines.py -h
-          python3 scripts/train_tox.py -h
+          python3 scripts/train_tox -h
+          chmod +x scripts/train_tox
+          scripts/train_tox -h
 
       - name: Send Slack notification
         uses: 8398a7/action-slack@v2

.github/workflows/push_pypi.yml

@@ -0,0 +1,23 @@
+name: Upload Python Package
+
+on:
+  release:
+    types: [created]
+
+jobs:
+  deploy:
+    runs-on: ubuntu-20.04
+    steps:
+      - uses: actions/checkout@v2
+      - uses: actions/setup-python@v2
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install setuptools wheel twine
+      - name: Build and publish
+        env:
+          TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }}
+          TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
+        run: |
+          python setup.py sdist bdist_wheel
+          twine upload --skip-existing dist/*

README.md

@@ -38,20 +38,18 @@ print(f"Clinical toxicitiy predictions: {clintox('CCO')}")
 ### Setup
 The library itself has few dependencies (see [setup.py](setup.py)) with loose requirements. 
 ```sh
-conda env create -f conda.yml
-conda activate toxsmi
 pip install -e .
 ```
 
 ### Start a training
 
-In the `scripts` directory is a training script [train_tox.py](./scripts/train_tox.py).
+In the `scripts` directory is a training script [train_tox](./scripts/train_tox).
 
 Download sample data from the Tox21 database and store it in a folder called `data`
 [here](https://ibm.box.com/s/kahxnlg2k2s0x3z0r5fa6y67tmfhs6or). 
 
 ```console
-(toxsmi) $ python3 scripts/train_tox.py \
+(toxsmi) $ python3 scripts/train_tox \
 --train data/tox21_train.csv \
 --test data/tox21_score.csv \
 --smi data/tox21.smi \
@@ -64,7 +62,7 @@ Download sample data from the Tox21 database and store it in a folder called `da
 - Set ```--finetune``` to the path to a `.pt` file to start from a pretrained model
 - Set ```--embedding_path``` to the path of pretrained embeddings
 
-Type `python scripts/train_tox.py -h` for further help.
+Type `python scripts/train_tox -h` for further help.
 
 ### Evaluate a model
 In the `scripts` directory is an evaluation script [eval_tox.py](./scripts/eval_tox.py).

requirements.txt

@@ -1,10 +1,9 @@
 paccmann_predictor @ git+https://github.com/PaccMann/paccmann_predictor@sarscov2
 numpy>=1.14.3
-torch>=1.5.1
-deepchem>=2.4
-six>=1.15.0
+torch
+six
 scikit-learn>=0.21.3
-tensorflow>=2.0
 Pillow>=7.1.0
 brc_pytorch>=0.1.3
-pytoda>=1.1.2
+rdkit
+pytoda>=1.1.5

scripts/eval_tox.py → scripts/eval_tox

@@ -1,4 +1,4 @@
-#!/usr/bin/env python3
+#! /usr/bin/env python3
 """Test toxsmi predictor."""
 import argparse
 import glob

scripts/train_tox.py → scripts/train_tox

@@ -1,4 +1,4 @@
-#!/usr/bin/env python3
+#! /usr/bin/env python3
 """Train toxsmi predictor."""
 import argparse
 import json

setup.py

@@ -30,14 +30,16 @@ def get_version(rel_path):
     author_email=("jab@zurich.ibm.com, greta.markert@gmail.com, drugilsberg@gmail.com"),
     install_requires=[
         "paccmann_predictor @ git+https://github.com/PaccMann/paccmann_predictor",
+        "numpy>=1.14.3",
         "torch",
-        "deepchem",
-        "tensorflow>=2.0",
         "Pillow",
         "six",
+        "scikit-learn>=0.21.3",
         "brc_pytorch>=0.1.3",
         "pytoda>=1.1.2",
+        "rdkit"
     ],
     packages=find_packages("."),
     zip_safe=False,
+    scripts=['scripts/train_tox', 'scripts/eval_tox']
 )

toxsmi/__init__.py

@@ -1,3 +1,3 @@
 """Initialization for `toxsmi` module."""
-__version__ = "0.0.3"
+__version__ = "1.0.0"
 __name__ = "toxsmi"

toxsmi/utils/__init__.py

@@ -1,5 +1,2 @@
 from .hyperparams import LOSS_FN_FACTORY  # noqa
-from .loaders import load_organdb_github  # noqa
-from .loaders import load_organdb_suppl  # noqa
-from .loaders import load_tox21  # noqa
 from .utils import *  # noqa