Zoo

.github/workflows/python-package.yml → .github/workflows/CI.yml

@@ -1,7 +1,7 @@
 # This workflow will install Python dependencies, run tests and lint with a variety of Python versions
 # For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
 
-name: Python package
+name: CI
 
 on:
   push:
@@ -17,30 +17,26 @@ jobs:
       matrix:
         python-version: [3.7, 3.8, 3.9]
 
-
-
-
     steps:
     - uses: actions/checkout@v2
     - name: Set up Python ${{ matrix.python-version }}
       uses: actions/setup-python@v2
       with:
         python-version: ${{ matrix.python-version }}
-    - uses: conda-incubator/setup-miniconda@v2
-      with:
-        installer-url: ${{ matrix.conda-installer }}
-        python-version: ${{ matrix.python-version }}
-        activate-environment: test
-        channel-priority: true
-        environment-file: devtools/conda-envs/malt.yaml
-        auto-activate-base: false
-        use-mamba: true
-    - name: Install dependencies
+    # - uses: conda-incubator/setup-miniconda@v2
+    #   with:
+    #     python-version: ${{ matrix.python-version }}
+    #     activate-environment: test
+    #     channel-priority: true
+    #     environment-file: devtools/conda-envs/malt.yaml
+    #     auto-activate-base: false
+    #     use-mamba: true
+    - name: Install dependencies and package
       run: |
         python -m pip install --upgrade pip
         python -m pip install flake8 pytest versioneer
         if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
-        python setup.py install
+        python -m pip install . --no-deps
     - name: Lint with flake8
       run: |
         # stop the build if there are Python syntax errors or undefined names

.github/workflows/sphinx.yml → .github/workflows/DOC.yml

@@ -1,5 +1,5 @@
-name: "Build Doc"
-on: 
+name: "DOC"
+on:
 - push
 
 jobs:
@@ -14,10 +14,8 @@ jobs:
     - name: Install dependencies and compile
       run: |
         python -m pip install --upgrade pip
-        python -m pip install flake8 pytest versioneer sphinx sphinx_rtd_theme
+        python -m pip install flake8 pytest versioneer sphinx sphinx_rtd_theme pyyaml networkx m2r2
         if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
-        pip install rdkit-pypi
-        pip install -e git+https://github.com/pytorch/pytorch_sphinx_theme.git#egg=pytorch_sphinx_theme
         python setup.py install
         cd docs && make html && cd _build/html && echo 'malt.wangyq.net' > CNAME
     - name: Deploy

.gitignore

@@ -129,10 +129,13 @@ dmypy.json
 .pyre/
 
 # data
-.bin
+*.bin
 
 # pytorch model
 .th
 
 # mac
 .DS_Store
+
+# performance
+*.csv

docs/conf.py

@@ -19,15 +19,15 @@
 sys.path.insert(0, os.path.abspath('..'))
 
 import malt
-from malt import agents, data, models, point, policy, trainer, utility_functions
+from malt import data, models, molecule, trainer, policy, agents, utils
 
 import os
-os.system("bash download_experiments.sh")
+# os.system("bash download_experiments.sh")
 
 # -- Project information -----------------------------------------------------
 
 project = 'malt'
-copyright = ("2020, Yuanqing Wang @ choderalab // MSKCC.")
+copyright = ("2022, Yuanqing Wang @ choderalab // MSKCC.")
 author = 'Yuanqing Wang'
 
 # The short X.Y version
@@ -171,7 +171,7 @@
 #  dir menu entry, description, category)
 texinfo_documents = [
     (master_doc, 'malt', 'malt Documentation',
-     author, 'malt', 'Extensible Surrogate Potential of Ab initio Learned and Optimized by Message-passing Algorithm',
+     author, 'malt', 'Molecular Active Learning Testbed',
      'Miscellaneous'),
 ]
 

docs/index.rst

@@ -12,7 +12,6 @@ MALT: Molecular Active Learning Testbed
 
    getting_started
    api
-   experiments/index
 
 
 

malt/__init__.py

@@ -1,3 +1,3 @@
-from . import data, models, point, trainer, policy, agents, metrics, utils
-from .point import Point
+from . import data, models, molecule, trainer, policy, agents, utils
+from .molecule import Molecule
 from .data.dataset import Dataset

malt/_version.py

@@ -41,8 +41,8 @@ def get_config():
     cfg.VCS = "git"
     cfg.style = "pep440"
     cfg.tag_prefix = ""
-    cfg.parentdir_prefix = "pinot-"
-    cfg.versionfile_source = "pinot/_version.py"
+    cfg.parentdir_prefix = "malt-"
+    cfg.versionfile_source = "malt/_version.py"
     cfg.verbose = False
     return cfg
 

malt/agents/__init__.py

@@ -1,3 +1,4 @@
+"""High-level abstraction of parties in molecular discovery."""
 from . import agent, assayer, merchant, player
 from .agent import Agent
 from .assayer import Assayer, DatasetAssayer

malt/agents/agent.py

@@ -1,3 +1,4 @@
+"""Base class of all agents."""
 import abc
 
 class Agent(abc.ABC):

malt/agents/assayer.py

@@ -1,3 +1,4 @@
+"""Agents that characterizes compounds."""
 import abc
 from .agent import Agent
 from malt.data.dataset import Dataset
@@ -45,7 +46,7 @@ def __init__(self, dataset: Dataset):
         super(DatasetAssayer, self).__init__()
         self.dataset = dataset
 
-    def assay(self, dataset):
+    def assay(self, dataset, by=['y']):
         """ Assay based on a given dataset.
 
         Parameters
@@ -59,10 +60,15 @@ def assay(self, dataset):
             Assayed dataset, with all `y` annotated.
 
         """
-        for point in dataset:
-            assert point in self.dataset
-            point.y = self.dataset[point].y
-            point.extra = self.dataset[point].extra
+        for molecule in dataset:
+
+            assert molecule in self.dataset
+
+            if molecule.metadata is None:
+                molecule.metadata = {}
+
+            for key in by:
+                molecule.metadata[key] = self.dataset[molecule].metadata[key]
 
         return dataset
 

malt/agents/merchant.py

@@ -1,3 +1,4 @@
+"""Agents that provide access to chemical spaces."""
 import abc
 from malt.data.dataset import Dataset
 from .agent import Agent
@@ -43,7 +44,7 @@ class DatasetMerchant(Merchant):
     >>> assert catalogue == dataset.clone().erase_annotation()
     >>> dataset_with_the_first_point = Dataset([dataset[0]])
     >>> dataset_merchant.merchandize(dataset_with_the_first_point)
-    Dataset with 1 points
+    Dataset with 1 molecules
     >>> assert len(dataset_merchant.dataset) == len(dataset) - 1
 
     """