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deepchem · Nov 26, 2020 · c9af5e5 · c9af5e5
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diff --git a/CONTRIBUTING.md → .github/CONTRIBUTING.md b/CONTRIBUTING.md → .github/CONTRIBUTING.md
diff --git a/.github/ISSUE_TEMPLATE/ISSUE_TEMPLATE.md b/.github/ISSUE_TEMPLATE/ISSUE_TEMPLATE.md
diff --git a/.github/ISSUE_TEMPLATE/bug_report.md b/.github/ISSUE_TEMPLATE/bug_report.md
@@ -0,0 +1,36 @@
+---
+name: "\U0001F41B Bug Report"
+about: Submit a bug report to help us improve DeepChem
+---
+
+## 🐛 Bug
+
+<!-- A clear and concise description of what the bug is. -->
+
+## To Reproduce
+
+Steps to reproduce the behavior:
+
+1.
+2.
+3.
+
+<!-- If you have a code sample, error messages, stack traces, please provide it here as well. -->
+
+## Expected behavior
+
+<!-- A clear and concise description of what you expected to happen. -->
+
+## Environment
+
+* OS:
+* Python version:
+* DeepChem version:
+* RDKit version (optional):
+* TensorFlow version (optional):
+* PyTorch version (optional):
+* Any other relevant information:
+
+## Additional context
+
+<!-- Add any other context about the problem here. -->
diff --git a/.github/ISSUE_TEMPLATE/feature_request.md b/.github/ISSUE_TEMPLATE/feature_request.md
@@ -0,0 +1,16 @@
+---
+name: "\U0001F680 Feature Request"
+about: Submit a proposal/request for a new DeepChem feature
+---
+
+## 🚀 Feature
+
+<!-- A clear and concise description of the feature proposal. Please provide a link to the paper and code in case they exist. -->
+
+## Motivation
+
+<!-- Please outline the motivation for the proposal. Is your feature request related to a problem? e.g., I'm always frustrated when [...]. If this is related to another GitHub issue, please link here too. -->
+
+## Additional context
+
+<!-- Add any other context or screenshots about the feature request here. -->
diff --git a/.github/ISSUE_TEMPLATE/installation.md b/.github/ISSUE_TEMPLATE/installation.md
@@ -0,0 +1,29 @@
+---
+name: "\U0001F4DA Installation"
+about: Report an installation problem with DeepChem
+---
+
+## 📚 Installation
+
+<!-- A clear and concise description of the installation error. If you have installation log file, please provide it here as well. -->
+
+## Environment
+
+* OS:
+* Pacakge manager (PyPI or Conda):
+* Python version:
+* TensorFlow version:
+* DeepChem version:
+* PyTorch version (optional):
+* CUDA/cuDNN version (optional):
+* Any other relevant information:
+
+## Checklist
+
+- [ ] I followed the [installation guide](https://deepchem.readthedocs.io/en/latest/get_started/installation.html).
+- [ ] I used Google Colab.
+- [ ] I do have multiple CUDA versions on my machine.
+
+## Additional context
+
+<!-- Add any other context about the problem here. -->
diff --git a/.github/ISSUE_TEMPLATE/question_help.md b/.github/ISSUE_TEMPLATE/question_help.md
@@ -0,0 +1,8 @@
+---
+name: "❓Questions & Help"
+about: Start a general discussion related to DeepChem
+---
+
+## ❓ Questions & Help
+
+<!-- A clear and concise description of the question. -->
diff --git a/...LL_REQUEST_TEMPLATE/molnet_pr_template.md → .github/MOLNET_PR_TEMPLATE.md b/...LL_REQUEST_TEMPLATE/molnet_pr_template.md → .github/MOLNET_PR_TEMPLATE.md
@@ -1,4 +1,5 @@
 ### Template for pull request contributing a new dataset to MoleculeNet
+
 Category: {Quantum Mechanics, Materials Science, Physical Chemistry, Biophysics, Physiology}  
 Dataset: {short name identifying dataset}  
 Data Type: {SMILES, 3D coordinates}  

diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md
@@ -0,0 +1,28 @@
+# Pull Request Template
+
+## Description
+
+Please include a summary of the change and which issue is fixed.
+Please also include relevant motivation and context.
+List any dependencies that are required for this change.
+
+Fix #(issue)
+
+## Type of change
+
+Please check the option that is related to your PR.
+
+- [ ] Bug fix (non-breaking change which fixes an issue)
+- [ ] New feature (non-breaking change which adds functionality)
+- [ ] Breaking change (fix or feature that would cause existing functionality to not work as expected)
+- [ ] Documentations (modification for documents)
+
+## Checklist
+
+- [ ] My code follows [the style guidelines of this project](https://deepchem.readthedocs.io/en/latest/development_guide/coding.html)
+- [ ] I have performed a self-review of my own code
+- [ ] I have commented my code, particularly in hard-to-understand areas
+- [ ] I have made corresponding changes to the documentation
+- [ ] I have added tests that prove my fix is effective or that my feature works
+- [ ] New and existing unit tests pass locally with my changes
+- [ ] I have checked my code and corrected any misspellings
diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
@@ -29,7 +29,7 @@ jobs:
     - name: Build DeepChem
       run: |
         python -m pip install --upgrade pip
-        pip install tensorflow==2.3.0
+        pip install tensorflow'>=2.3,<2.4'
         pip install -e .
     - name: Import checking
       run: python -c "import deepchem"

diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
@@ -26,7 +26,7 @@ jobs:
     - name: Build DeepChem
       run: |
         python -m pip install --upgrade pip
-        pip install tensorflow==2.3.0
+        pip install tensorflow'>=2.3,<2.4'
         pip install -e .
     - name: Import checking
       run: python -c "import deepchem"

diff --git a/README.md b/README.md
@@ -21,11 +21,8 @@ materials science, quantum chemistry, and biology.
   - [Docker](#docker)
   - [From source](#from-source)
 - [Getting Started](#getting-started)
-- [Contributing to DeepChem](/CONTRIBUTING.md)
-  - [Code Style Guidelines](/CONTRIBUTING.md#code-style-guidelines)
-  - [Documentation Style Guidelines](/CONTRIBUTING.md#documentation-style-guidelines)
-  - [Gitter](#gitter)
 - [About Us](#about-us)
+- [Contributing to DeepChem](/.github/CONTRIBUTING.md)
 - [Citing DeepChem](#citing-deepchem)
 
 ## Requirements
@@ -44,7 +41,7 @@ DeepChem currently supports Python 3.6 through 3.7 and requires these packages o
 ### Soft Requirements
 
 DeepChem has a number of "soft" requirements.  
-If you face some errors like `ImportError: No module named XXXX`, you may need to install some packages.
+If you face some errors like `ImportError: This class requires XXXX`, you may need to install some packages.
 
 Please check [the document](https://deepchem.readthedocs.io/en/latest/requirements.html##soft-requirements) about soft requirements.
 
@@ -140,7 +137,3 @@ To cite this book, please use this bibtex entry:
     year={2019}
 }
 ```
-
-## Version
-
-2.4.0-rc
diff --git a/deepchem/__init__.py b/deepchem/__init__.py
@@ -3,7 +3,7 @@
 """
 
 # If you push the tag, please remove `.dev`
-__version__ = '2.4.0-rc1.dev'
+__version__ = '2.4.0.dev'
 
 import deepchem.data
 import deepchem.feat

diff --git a/deepchem/feat/molecule_featurizers/mol_graph_conv_featurizer.py b/deepchem/feat/molecule_featurizers/mol_graph_conv_featurizer.py
@@ -184,7 +184,7 @@ def _featurize(self, mol: RDKitMol) -> GraphData:
           from rdkit.Chem import AllChem
           AllChem.ComputeGasteigerCharges(mol)
         except ModuleNotFoundError:
-          raise ImportError("This method requires RDKit to be installed.")
+          raise ImportError("This class requires RDKit to be installed.")
 
     # construct atom (node) feature
     h_bond_infos = construct_hydrogen_bonding_info(mol)

diff --git a/docs/requirements.txt b/docs/requirements.txt
@@ -2,6 +2,6 @@ pandas
 scikit-learn
 sphinx>=3.2,<4
 sphinx_rtd_theme>=0.5,<1
-tensorflow==2.3.0
+tensorflow>=2.3,<2.4
 transformers
 torch==1.6.0
diff --git a/docs/source/api_reference/moleculenet.rst b/docs/source/api_reference/moleculenet.rst
@@ -227,7 +227,7 @@ UV Datasets
 .. _`deepchem.molnet.load_function.load_dataset_template`: https://github.com/deepchem/deepchem/blob/master/deepchem/molnet/load_function/load_dataset_template.py
 .. _`deepchem.molnet.defaults`: https://github.com/deepchem/deepchem/tree/master/deepchem/molnet/defaults.py
 .. _`deepchem.molnet.__init__.py`: https://github.com/deepchem/deepchem/blob/master/deepchem/molnet/__init__.py
-.. _`template`: https://github.com/deepchem/deepchem/blob/master/.github/PULL_REQUEST_TEMPLATE/molnet_pr_template.md
+.. _`template`: https://github.com/deepchem/deepchem/blob/master/.github/MOLNET_PR_TEMPLATE.md
 
 ZINC15 Datasets
 ---------------

diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -127,5 +127,5 @@ def find_source():
   except Exception:
     filename = info['module'].replace('.', '/') + '.py'
 
-  tag = 'master' if 'dev' in release else ('v' + release)
+  tag = 'master' if 'dev' in release else release
   return "https://github.com/deepchem/deepchem/blob/%s/%s" % (tag, filename)
diff --git a/docs/source/development_guide/infra.rst b/docs/source/development_guide/infra.rst
@@ -5,39 +5,34 @@ The DeepChem project maintains supporting infrastructure on a number of
 different services. This infrastructure is maintained by the DeepChem
 development team.
 
-Github
+GitHub
 ------
 The core DeepChem repositories are maintained in the `deepchem`_ GitHub organization.
+And, we use GitHub Actions to build a continuous integration pipeline.
 
 .. _`deepchem`: https://github.com/deepchem
 
 DeepChem developers have write access to the repositories on this repo and 
 technical steering committee members have admin access.
 
-Travis CI
----------
-DeepChem runs continuous integration tests on `Travis CI`_.
-
-.. _`Travis CI`: https://travis-ci.org/github/deepchem
-
 Conda Forge
 -----------
-The DeepChem `feedstock`_ repo maintains the build recipe for Conda-Forge.
+The DeepChem `feedstock`_ repo maintains the build recipe for conda-forge.
 
 .. _`feedstock`: https://github.com/conda-forge/deepchem-feedstock
 
 
-Dockerhub
----------
-DeepChem hosts major releases and nightly docker build instances on `dockerhub`_.
+Docker Hub
+----------
+DeepChem hosts major releases and nightly docker build instances on `Docker Hub`_.
 
-.. _`dockerhub`: https://hub.docker.com/r/deepchemio/deepchem
+.. _`Docker Hub`: https://hub.docker.com/r/deepchemio/deepchem
 
-PyPi
+PyPI
 ----
-DeepChem hosts major releases and nightly builds on `pypi`_.
+DeepChem hosts major releases and nightly builds on `PyPI`_.
 
-.. _`pypi`: https://pypi.org/project/deepchem/
+.. _`PyPI`: https://pypi.org/project/deepchem/
 
 Amazon Web Services
 -------------------

diff --git a/docs/source/get_started/requirements.rst b/docs/source/get_started/requirements.rst
@@ -23,7 +23,7 @@ Soft requirements
 DeepChem has a number of "soft" requirements.
 
 +--------------------------------+---------------+---------------------------------------------------+
-| Package name                   | Version       | Location where this package is imported           |
+| Package name                   | Version       | Location where this package is used               |
 |                                |               | (dc: deepchem)                                    |
 +================================+===============+===================================================+
 | `BioPython`_                   | latest        | :code:`dc.utlis.genomics_utils`                   |

diff --git a/CODE_OF_CONDUCT.md → notes/code_of_conduct.md b/CODE_OF_CONDUCT.md → notes/code_of_conduct.md
diff --git a/notes/relaease.md b/notes/relaease.md
@@ -0,0 +1,51 @@
+# Release
+
+This note explains how to release deepchem packages.
+
+## How to release
+
+1. Create and merge a release PR (just modify the version in `deepchem/__init__.py`)
+2. Push a new tag in a merge commit -> release in PyPI 
+3. Create and merge a release PR in the [feedstock repository](https://github.com/conda-forge/deepchem-feedstock) -> release in conda forge
+4. Create and merge a PR for updating the Dockerfile (`docker/conda-forge/Dockerfile`)
+5. Build and publish a new docker image -> release in DockerHub 
+6. Fix the version in README.md and Documentation
+
+## PyPI
+
+### Nightly build
+
+We publish the nightly build only when merging a PR to the master and passing all CI checks in a merge commit.
+**If some CI check doesn't pass in a merge commit, the nightly build package will not be published.**
+The publish process is automated by GitHub Actions and it is in `deploy` section of `.github/workflows/main.yml`.
+
+### Major version build
+
+We publish the major version build only when pushing a new tag.
+The publish process is automated by GitHub Actions and it is in `.github/workflows/release.yml`.
+
+## Conda Forge
+
+We have [the feedstock repository](https://github.com/conda-forge/deepchem-feedstock) for managing the build recipe for conda-forge.
+After pushing a new tag, we create a PR for publishing a new build.
+Basically, we need to modify the version of deepchem and dependencies like TensorFlow in `recipe/meta.yml`.
+After merging a PR, we could publish a new package.
+
+## Docker
+
+### Nightly build
+
+The latest tag (deepchemio/deepchem:latest) is the nightly build and the image is built by `docker/master/Dockerfile`.
+We publish the nightly build only when merging a PR to the master.
+The publish process is automated by [Docker Hub](https://docs.docker.com/docker-hub/builds/).
+
+### Major version build
+
+The specific tag (deepchemio/deepchem:2.3.0) is the major version build and the image is built by `docker/conda-forge/Dockerfile`.
+After publishing the new conda package, we need to modify `docker/conda-forge/Dockerfile`, build and publish the new image manually.
+
+```bash
+$ cd docker/conda-forge
+$ docker build . -t deepchem:X.X.X
+$ docker push deepchem:X.X.X
+```
diff --git a/setup.py b/setup.py
@@ -18,9 +18,14 @@ def _get_version():
         g = {}
         exec(line, g)
         base = g['__version__']
-        # nightly version string .devYearMonthDayHourMinute
-        return base if IS_RELEASE else \
-          base + time.strftime("%Y%m%d%H%M%S")
+        if IS_RELEASE:
+          return base
+        else:
+          # nightly version : .devYearMonthDayHourMinute
+          if base.endswith('.dev') is False:
+            # Force to add `.dev` if `--release` option isn't passed when building
+            base += '.dev'
+          return base + time.strftime("%Y%m%d%H%M%S")
 
     raise ValueError('`__version__` not defined in `deepchem/__init__.py`')