chore: refactor the repository

brsynth · Oct 13, 2021 · d39aac0 · d39aac0
1 parent 3be6f15
commit d39aac0
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diff --git a/.github/workflows/check.yml b/.github/workflows/check.yml
@@ -6,19 +6,11 @@ name: Check
 on:
 
   push:
-    branches: [ master, dev ]
-    paths-ignore:
-      - '**/RELEASE*'
-      - '**/README*'
-      - '**/LICENSE*'
-      - 'recipe'
-      - 'docs'
-      - '.gitignore'
-      - '.github'
-      - '!.github/workflows/check*'
-      - '**/_version.py'
+    branches: [ main, master, dev ]
+    paths:
+      - '**.py'
   pull_request:
-    branches: [ master ]
+    branches: [ main, master ]
 
 jobs:
 
@@ -39,4 +31,5 @@ jobs:
     - name: Checking package
       run: |
         cd ci
-        make check-inconda
+        make check-buildenv env=check
+        conda run -n check make check
diff --git a/.github/workflows/publish.yml b/.github/workflows/publish.yml
@@ -2,44 +2,119 @@ name: Publish
 
 on:
   push:
-    tags: releases/[1-9]+.[0-9]+.[0-9]+
-    branches: [ stable ]
+    branches:
+      - stable
+    paths:
+      - '**.py'
+      - '!tests/**'
 
 jobs:
 
-  Publish:
+  Conda-Build_Test:
     runs-on: ubuntu-latest
-
-    env:
-      ANACONDA_TOKEN: ${{secrets.ANACONDA_TOKEN}}
-      ANACONDA_USER: ${{secrets.ANACONDA_USER}}
-
     steps:
     - uses: actions/checkout@v2
-    - uses: docker://continuumio/miniconda3
-
-    - name: Updating conda
-      run: conda update --all -y
-
     - name: Installing make
-      run: conda install -y make
-
-    - name: Building package
+      run: |
+        sudo apt-get update
+        sudo apt-get -y install make
+    - name: Build conda package
       run: |
         cd ci
         make conda-build
-
-    - name: Testing package
+    - name: Test conda package
       run: |
         cd ci
         make conda-test
 
-    - name: Converting to other platforms
-      run: |
-        cd ci
-        make conda-convert
+  Tag:
+    needs: [Conda-Build_Test]
+    runs-on: ubuntu-latest
+    outputs: # Create variable usable from another job
+      new_tag: ${{ steps.tag_version.outputs.new_tag }}
+    steps:
+      ## CREATE TAG/RELEASE
+      - uses: actions/checkout@v2
+        with:
+          persist-credentials: false # otherwise, the token used is the GITHUB_TOKEN, instead of your personal access token.
+          fetch-depth: 0 # otherwise, there would be errors pushing refs to the destination repository.
+      - name: Bump version and push tag
+        id: tag_version
+        uses: mathieudutour/github-tag-action@v5.6
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          release_branches: stable
+          tag_prefix:
+      - name: Create Release
+        uses: actions/create-release@v1
+        with:
+          tag_name: ${{ steps.tag_version.outputs.new_tag }}
+          release_name: Release ${{ steps.tag_version.outputs.new_tag }}
+          body: ${{ steps.tag_version.outputs.changelog }}
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+      ## UPDATE CHANGELOG
+      - uses: actions/checkout@v2
+        with:
+          persist-credentials: false # otherwise, the token used is the GITHUB_TOKEN, instead of your personal access token.
+          fetch-depth: 0 # otherwise, there would be errors pushing refs to the destination repository.
+      - uses: actions/setup-ruby@v1
+        # with:
+        #   ruby-version: '2.6' # Version range or exact version of a Ruby version to use, using semvers version range syntax.
+      - name: Generate CHANGELOG
+        env:
+          CHANGELOG_GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        run: |
+          gem install github_changelog_generator
+          github_changelog_generator -u brsynth -p rrparser --no-unreleased
+      - name: Update _version.py
+        env:
+          CHANGELOG_GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          TAG: ${{ steps.tag_version.outputs.new_tag }}
+        run: |
+          folder=`dirname $(find . -name _version.py)`
+          echo "__version__ = \"$TAG\"" > $folder/_version.py
+      - name: Commit files
+        run: |
+          git config --local user.email "$GITHUB_EMAIL"
+          git config --local user.name "$GITHUB_USERNAME"
+          git commit -m "doc(CHANGELOG): update" -a
+        env:
+          GITHUB_USERNAME: brsynth
+          GITHUB_EMAIL: joan.herisson@univ-evry.fr
+      - name: Push changes
+        uses: ad-m/github-push-action@master
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          branch: ${{ github.ref }}
 
-    - name: Uploading to anaconda
-      run: |
-        cd ci
-        make conda-publish
+  ## UPDATE CONDA-FORGE FEEDSTOCK
+  Feedstock:
+    needs: [Tag]
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout feedstock fork
+        uses: actions/checkout@v2
+        with:
+          repository: conda-forge/rrparser-feedstock
+          persist-credentials: false
+          fetch-depth: 0
+      - name: Update recipe
+        run: |
+          wget -O- https://github.com/brsynth/rrparser/archive/refs/tags/$VERSION.tar.gz | shasum -a 256 > sha.txt
+          sha=`python -c "f = open('sha.txt'); print(f.read().split()[0]); f.close()"`
+          rm -f sha.txt
+          sed -i -E "s/(\{% set version = \")[^>]+(\" %\})/\1$VERSION\2/" recipe/meta.yaml
+          sed -i -E "s/(sha256: )[^>]+/\1$sha/" recipe/meta.yaml
+          git config --local user.email "$GITHUB_EMAIL"
+          git config --local user.name "$GITHUB_USERNAME"
+          git commit -m "chore(meta.yml): update version" -a
+        env:
+          GITHUB_USERNAME: brsynth
+          GITHUB_EMAIL: joan.herisson@univ-evry.fr
+          VERSION: ${{ needs.tag.outputs.new_tag }}
+      - name: Create Pull Request
+        uses: peter-evans/create-pull-request@v3
+        with:
+          token: ${{ secrets.FEEDSTOCK }}
+          push-to-fork: brsynth/rrparser-feedstock
diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
@@ -6,19 +6,11 @@ name: Test
 on:
 
   push:
-    branches: [ master, dev ]
-    paths-ignore:
-      - '**/RELEASE*'
-      - '**/README*'
-      - '**/LICENSE*'
-      - 'recipe'
-      - 'docs'
-      - '.gitignore'
-      - '.github'
-      - '!.github/workflows/test*'
-      - '**/_version.py'
+    branches: [ main, master, dev ]
+    paths:
+      - '**.py'
   pull_request:
-    branches: [ master ]
+    branches: [ main, master ]
 
 jobs:
 
@@ -39,4 +31,5 @@ jobs:
     - name: Testing package
       run: |
         cd ci
-        make test-inconda
+        make test-buildenv env=test
+        conda run -n test make test
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -0,0 +1,3 @@
+# Changelog
+
+## [2.4.1]
diff --git a/README.md b/README.md
@@ -1,8 +1,11 @@
-# RRParser
+# rrparser
+Reaction Rules Parser
+| Name | Downloads | Version | Platforms |
+| --- | --- | --- | --- |
+| [![Conda Recipe](https://img.shields.io/badge/recipe-rrparser-green.svg)](https://anaconda.org/conda-forge/rrparser) | [![Conda Downloads](https://img.shields.io/conda/dn/conda-forge/rrparser.svg)](https://anaconda.org/conda-forge/rrparser) | [![Conda Version](https://img.shields.io/conda/vn/conda-forge/rrparser.svg)](https://anaconda.org/conda-forge/rrparser) | [![Conda Platforms](https://img.shields.io/conda/pn/conda-forge/rrparser.svg)](https://anaconda.org/conda-forge/rrparser) |
 
-[![Anaconda-Server Badge](https://anaconda.org/brsynth/rrparser/badges/latest_release_date.svg)](https://anaconda.org/brsynth/rrparser) ![Test](https://github.com/brsynth/RRulesParser/workflows/Test/badge.svg) [![Anaconda-Server Badge](https://anaconda.org/brsynth/rrparser/badges/version.svg)](https://anaconda.org/brsynth/rrparser)
-
-Reaction Rules Parser. If no input reaction files is provided, retrieves the reaction rules from [RetroRules](https://retrorules.org).
+## Description
+*Reaction Rules Parser*. If no input reaction files is provided, retrieves the reaction rules from [RetroRules](https://retrorules.org).
 
 ## Input
 
@@ -17,7 +20,7 @@ Reaction Rules Parser. If no input reaction files is provided, retrieves the rea
 ## Install
 ### From Conda
 ```sh
-[sudo] conda install -c brsynth rrparser
+[sudo] conda install -c conda-forge rrparser
 ```
 
 ## Use
@@ -26,12 +29,14 @@ Reaction Rules Parser. If no input reaction files is provided, retrieves the rea
 ```python
 from rrparser import parse_rules
 
-outfile = parse_rules(<rules_file>,
-                      <outfile>,
-                      input_format=<'csv' | 'tsv'>,
-                      rule_type=<'all' | 'retro' | 'forward'>,
-                      diameters=<'2,4,6,8,10,12,14,16'>,
-                      output_format=<'csv' | 'tsv'>)
+outfile = parse_rules(
+  <rules_file>,
+  <outfile>,
+  input_format=<'csv' | 'tsv'>,
+  rule_type=<'all' | 'retro' | 'forward'>,
+  diameters=<'2,4,6,8,10,12,14,16'>,
+  output_format=<'csv' | 'tsv'>
+)
 ```
 
 If parameters from CLI have to be parsed, the function `build_args_parser` is available:
@@ -59,8 +64,7 @@ Test can be run with the following commands:
 
 ### Natively
 ```bash
-cd tests
-pytest -v
+python -m pytest -v
 ```
 
 # CI/CD

diff --git a/ci/.env → ci/.ci_env b/ci/.env → ci/.ci_env
diff --git a/ci/LICENSE b/ci/LICENSE
@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) 2020 Jean-Loup Faulon's group & INRA
+Copyright (c) 2020 Jean-Loup Faulon's group & INRAE
 Copyright (c) 2020 University of Evry / Paris-Saclay
 
 Permission is hereby granted, free of charge, to any person obtaining a copy

diff --git a/ci/Makefile b/ci/Makefile
@@ -1,8 +1,9 @@
 SHELL := /bin/bash
 SELF_DIR := $(dir $(lastword $(MAKEFILE_LIST)))
+PACKAGE = $(shell python ../setup.py --name)
+
+include $(SELF_DIR)/.ci_env
 
-include $(SELF_DIR)/.env
-include $(SELF_DIR)/../extras/.env
 
 # HELP
 # This will output the help for each task
@@ -34,14 +35,20 @@ check: ## Test code with 'pytest', this is the fastest way to test the code
 test: ## Test code with 'pytest', this is the fastest way to test the code
 	   @$(MAKE_CMD) -f test.mk test args="$(args)"
 
-%-inconda: ## Test conda package
+%-buildenv: ## Test conda package
 ifneq ($(strip $(env)),)
 	$(eval env=${PACKAGE}_$*)
 endif
-	@$(MAKE_CMD) -f conda.mk check-environment-$* env=$(env)
-	@$(MAKE_CMD) -f conda.mk conda-run-env env=$(env) \
-										   cmd="make -C .. $*" \
-										   args="$(args)"
+	@$(MAKE_CMD) -f conda.mk build-environment-$* env=$(env)
+
+# %-inconda: ## Test conda package
+# ifneq ($(strip $(env)),)
+# 	$(eval env=${PACKAGE}_$*)
+# endif
+# 	@$(MAKE_CMD) -f conda.mk check-environment-$* env=$(env)
+# 	@$(MAKE_CMD) -f conda.mk conda-run-env env=$(env) \
+# 										   cmd="make -C .. $*" \
+# 										   args="$(args)"
 
 
 conda-all: conda-build conda-test conda-convert conda-publish ## (default) Perform all conda process (build, test, convert, publish)
@@ -64,3 +71,6 @@ conda-check-recipe: ## Check conda recipe
 
 conda-create-run_env: ## Make an conda environment to run program
 	@$(MAKE_CMD) -f conda.mk check-environment-test env=${PACKAGE}_test
+
+doc-pdoc:
+	cd .. ; rm -rf chemlite/__pycache__ ; pdoc --force --html -o docs chemlite