chore: refactor repo

brsynth · Oct 14, 2021 · 68c3541 · 68c3541
1 parent b94a030
commit 68c3541
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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/[email protected]
+        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 rxn_rebuild --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: [email protected]
+      - 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/rxn_rebuild-feedstock
+          persist-credentials: false
+          fetch-depth: 0
+      - name: Update recipe
+        run: |
+          wget -O- https://github.com/brsynth/rxn_rebuild/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: [email protected]
+          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/rxn_rebuild-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
+
+## [2.1.0]
diff --git a/MANIFEST.in b/MANIFEST.in
@@ -1 +0,0 @@
-recursive-include rxn_rebuild/workflows *

diff --git a/README.md b/README.md
@@ -1,3 +1,13 @@
+# rxn_rebuild
+Rebuild full reaction from reaction rule
+| Name | Downloads | Version | Platforms |
+| --- | --- | --- | --- |
+| [![Conda Recipe](https://img.shields.io/badge/recipe-rxn_rebuild-green.svg)](https://anaconda.org/conda-forge/rxn_rebuild) | [![Conda Downloads](https://img.shields.io/conda/dn/conda-forge/rxn_rebuild.svg)](https://anaconda.org/conda-forge/rxn_rebuild) | [![Conda Version](https://img.shields.io/conda/vn/conda-forge/rxn_rebuild.svg)](https://anaconda.org/conda-forge/rxn_rebuild) | [![Conda Platforms](https://img.shields.io/conda/pn/conda-forge/rxn_rebuild.svg)](https://anaconda.org/conda-forge/rxn_rebuild) |
+
+## Description
+*rxn_rebuild* provides a cache for RetroRules and MetaNetX compounds and reactions
+
+
 # rxn_rebuild
 
 [![Anaconda-Server Badge](https://anaconda.org/brsynth/rxn_rebuild/badges/latest_release_date.svg)](https://anaconda.org/brsynth/rxn_rebuild) [![Anaconda-Server Badge](https://anaconda.org/brsynth/rxn_rebuild/badges/version.svg)](https://anaconda.org/brsynth/rxn_rebuild)
@@ -22,28 +32,12 @@ Rebuild full reaction from a reaction rule ID and a chemical transformation by a
     - values: infos (SMILES, InChI, InChIKey, formula, name)
 
 
-## Prerequisites
-
-* Python 3
-
 ## Install
 
-### Prerequisite
-
 The conda package manager is required. Fresh instructions on how to install conda are [available online](https://docs.conda.io/projects/conda/en/latest/user-guide/install/).
 
-### conda environment
-
-In case a new conda environment `<my_env>` need to be set up, first start with:
-```shell
-conda create -n my_env python=3
-```
-
-### conda package
-
-Install in the `<my_env>` conda environment:
 ```shell
-conda install -c brsynth -c conda-forge -n <my_env> rxn_rebuild 
+conda install -c conda-forge rxn_rebuild 
 ```
 
 ## Run
@@ -55,17 +49,15 @@ python -m rxn_rebuild <rxn_rule_id> <transfo> [<ori_rxn_id>]
 ```
 **From Python code**
 ```python
-from rr_cache import rrCache
 from rxn_rebuild import rebuild_rxn, build_args_parser
 
 parser = build_args_parser()
 args   = parser.parse_args()
 
 completed_transfos = rebuild_rxn(
-    cache = rrCache(attrs=['rr_reactions', 'template_reactions','cid_strc']),
-    rxn_rule_id = args.rxn_rule_id,
-    transfo = args.trans_smi,
-    tmpl_rxn_id = args.ori_rxn_id
+    rxn_rule_id=args.rxn_rule_id,
+    transfo=args.trans_smi,
+    tmpl_rxn_id=args.ori_rxn_id
 )
 ```
 If `cache` is not provided, it ill be automatically loaded within `rebuild_rxn` function but it could be much slower if called inside a loop.

diff --git a/ci/.env → ci/.ci_env b/ci/.env → ci/.ci_env
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)
@@ -66,10 +73,4 @@ 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
-
-doc-sphinx:
-	cd .. ; sphinx-apidoc -f -o docs/source chemlite
-
-doc-sphinx-html:
-	cd ../docs ; make html
+	cd .. ; rm -rf chemlite/__pycache__ ; pdoc --force --html -o docs chemlite