Merge branch 'feature/conda-cache' into develop

.github/workflows/docs.yaml

@@ -9,14 +9,18 @@ jobs:
   deploy:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - if: ${{ github.ref == 'refs/heads/develop' }} #we delay develop because when we release a hotgix (tag + develop push), one of these push will be out of sync
+        uses: jakejarvis/wait-action@master
         with:
-          fetch-depth: 0
+          time: '60s'
       - uses: actions/setup-python@v2
         with:
           python-version: 3.x
       - run: pip install git+https://${GH_TOKEN}@github.com/carissalow/mkdocs-material-insiders.git
       - run: pip install mike
+      - uses: actions/checkout@v2
+        with:
+          fetch-depth: 0
       - run: |
           git config user.name github-actions
           git config user.email github-actions@github.com

.github/workflows/tests.yaml

@@ -2,7 +2,13 @@ name: tests
 
 on:
   push:
-    #branches: [ develop ]
+    branches-ignore:
+      - "master"
+    tags:
+      - "v[0-9]+.[0-9]+.[0-9]+"
+  pull_request:
+    branches:
+      - "develop"
 env:
   RENV_PATHS_ROOT: ~/.local/share/renv
 
@@ -13,31 +19,60 @@ jobs:
       - uses: actions/checkout@v2
         with:
           fetch-depth: 0
-      - uses: s-weigand/setup-conda@v1
-      - run : conda --version
-      - run : source activate base
+      - run: "sed -i 's/name:.*/name: rapidstests/g' environment.yml"
+      - run: echo "RELEASE_VERSION=${GITHUB_REF#refs/*/}" >> $GITHUB_ENV
+      - run: echo "RELEASE_VERSION_URL=$(echo $RELEASE_VERSION | sed -e 's/\.//g')" >> $GITHUB_ENV
       - run : |
           sudo apt update
-          sudo apt install libcurl4-openssl-dev
-          sudo apt install libssl-dev
-          sudo apt install libxml2-dev
+          # sudo apt install libcurl4-openssl-dev
+          # sudo apt install libssl-dev
+          # sudo apt install libxml2-dev
           sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9
           sudo add-apt-repository 'deb https://cloud.r-project.org/bin/linux/ubuntu focal-cran40/' 
           sudo apt install r-base
-          sudo apt install pandoc
-          sudo Rscript --vanilla -e 'install.packages("rmarkdown", repos="http://cran.us.r-project.org")'
-          conda env create -f environment.yml -n test-environment
-          source activate test-environment
-      - name: Cache packages
+      - name: Cache R packages
         uses: actions/cache@v1
         with:
           path: ${{ env.RENV_PATHS_ROOT }}
           key: ${{ runner.os }}-renv-${{ hashFiles('**/renv.lock') }}
           restore-keys: |
             ${{ runner.os }}-renv-
-      - name: Restore packages
+      - name: Restore R packages
         shell: Rscript {0}
         run: |
           if (!requireNamespace("renv", quietly = TRUE)) install.packages("renv")
           renv::restore()
-      - run : bash tests/scripts/run_tests.sh all test 
+      - name: Cache conda packages
+        uses: actions/cache@v1
+        env:
+          # Increase this value to reset cache if environment.yml has not changed
+          CACHE_NUMBER: 0
+        with:
+          path: ~/conda_pkgs_dir
+          key:
+            ${{ runner.os }}-conda-${{ env.CACHE_NUMBER }}-${{
+            hashFiles('**/environment.yml') }}
+      - name: Restore conda packages
+        uses: conda-incubator/setup-miniconda@v2
+        with:
+          activate-environment: rapidstests
+          environment-file: environment.yml
+          use-only-tar-bz2: true # IMPORTANT: This needs to be set for caching to work properly!
+      - name: Run tests
+        shell: bash -l {0}
+        run : |
+            conda activate rapidstests
+            bash tests/scripts/run_tests.sh all test 
+      - name: Release tag
+        if: success() && startsWith(github.ref, 'refs/tags')
+        id: create_release
+        uses: actions/create-release@v1
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} # This token is provided by Actions, you do not need to create your own token
+        with:
+          tag_name: ${{ github.ref }}
+          release_name: ${{ github.ref }}
+          body: |
+            See [change log](http://www.rapids.science/latest/change-log/#${{ env.RELEASE_VERSION_URL }})
+          draft: false
+          prerelease: false

config.yaml

@@ -193,7 +193,7 @@ PHONE_KEYBOARD:
   TABLE: keyboard
   PROVIDERS:
     RAPIDS:
-      COMPUTE: True
+      COMPUTE: False
       FEATURES: []
       SRC_FOLDER: "rapids" # inside src/features/phone_keyboard
       SRC_LANGUAGE: "python"

docs/developers/git-flow.md

@@ -30,7 +30,7 @@ git commit -m "Add my new feature" # use a concise description
 
     ```bash
     git checkout feature/feature1
-    git pull origin develop
+    git fetch origin develop
     git rebase -i develop
     git checkout develop
     git merge --no-ff feature/feature1 # (use the default merge message)

docs/workflow-examples/analysis.md

@@ -37,7 +37,7 @@ In total, our example workflow has nine steps that are in charge of sensor data
 
 ## Configure and run the analysis workflow example
 1.	[Install](../../setup/installation) RAPIDS
-2.	Configure the [user credentials](../../setup/configuration/#database-credentials) of a local or remote MySQL server with writing permissions in your `.env` file. The example config file is at `example_profile/example_config.yaml`.
+2.	Configure the [user credentials](../../setup/configuration/#database-credentials) of a local or remote MySQL server with writing permissions in your `.env` file. The config file where you need to modify the `DATABASE_GROUP` is at `example_profile/example_config.yaml`.
 3.	Unzip the [test database](https://osf.io/skqfv/files/) to `data/external/rapids_example.sql` and run:
     ```bash
     ./rapids -j1 restore_sql_file --profile example_profile

tools/environment-from-history.yml

@@ -0,0 +1,17 @@
+name: devtest
+channels:
+  - defaults
+dependencies:
+  - python=3.7
+  - pandas=1.1.5
+  - scipy=1.5.2
+  - plotly=4.14.1
+  - astropy=4.2
+  - scikit-learn=0.23.2
+  - xgboost=0.90
+  - lightgbm=3.1.1
+  - conda-forge::imbalanced-learn=0.6.2
+  - pip=20.3.3
+  - pip:
+    - snakemake==5.30.2
+prefix: /usr/local/Caskroom/miniconda/base/envs/devtest