Merging master

Author: alexhlim

.github/ISSUE_TEMPLATE/documentation_improvement.md

@@ -9,7 +9,7 @@ labels: "Docs, Needs Triage"
 
 #### Location of the documentation
 
-[this should provide the location of the documentation, e.g. "pandas.read_csv" or the URL of the documentation, e.g. "https://dev.pandas.io/docs/reference/api/pandas.read_csv.html"]
+[this should provide the location of the documentation, e.g. "pandas.read_csv" or the URL of the documentation, e.g. "https://pandas.pydata.org/docs/reference/api/pandas.read_csv.html"]
 
 **Note**: You can check the latest versions of the docs on `master` [here](https://pandas.pydata.org/docs/dev/).
 

.github/PULL_REQUEST_TEMPLATE.md

@@ -1,5 +1,4 @@
 - [ ] closes #xxxx
 - [ ] tests added / passed
-- [ ] passes `black pandas`
-- [ ] passes `git diff upstream/master -u -- "*.py" | flake8 --diff`
+- [ ] Ensure all linting tests pass, see [here](https://pandas.pydata.org/pandas-docs/dev/development/contributing.html#code-standards) for how to run them
 - [ ] whatsnew entry

.github/actions/build_pandas/action.yml

@@ -0,0 +1,17 @@
+name: Build pandas
+description: Rebuilds the C extensions and installs pandas
+runs:
+  using: composite
+  steps:
+
+    - name: Environment Detail
+      run: |
+        conda info
+        conda list
+      shell: bash -l {0}
+
+    - name: Build Pandas
+      run: |
+        python setup.py build_ext -j 2
+        python -m pip install -e . --no-build-isolation --no-use-pep517
+      shell: bash -l {0}

.github/actions/setup/action.yml

@@ -0,0 +1,12 @@
+name: Set up pandas
+description: Runs all the setup steps required to have a built pandas ready to use
+runs:
+  using: composite
+  steps:
+    - name: Setting conda path
+      run: echo "${HOME}/miniconda3/bin" >> $GITHUB_PATH
+      shell: bash -l {0}
+
+    - name: Setup environment and build pandas
+      run: ci/setup_env.sh
+      shell: bash -l {0}

.github/workflows/ci.yml

@@ -2,74 +2,74 @@ name: CI
 
 on:
   push:
-    branches: master
+    branches: [master]
   pull_request:
     branches:
       - master
       - 1.2.x
 
 env:
   ENV_FILE: environment.yml
+  PANDAS_CI: 1
 
 jobs:
   checks:
     name: Checks
     runs-on: ubuntu-latest
-    steps:
-
-    - name: Setting conda path
-      run: echo "${HOME}/miniconda3/bin" >> $GITHUB_PATH
+    defaults:
+      run:
+        shell: bash -l {0}
 
+    steps:
     - name: Checkout
       uses: actions/checkout@v1
 
     - name: Looking for unwanted patterns
       run: ci/code_checks.sh patterns
       if: always()
 
-    - name: Setup environment and build pandas
-      run: ci/setup_env.sh
-      if: always()
+    - name: Cache conda
+      uses: actions/cache@v2
+      with:
+        path: ~/conda_pkgs_dir
+        key: ${{ runner.os }}-conda-${{ hashFiles('${{ env.ENV_FILE }}') }}
+
+    - uses: conda-incubator/setup-miniconda@v2
+      with:
+        activate-environment: pandas-dev
+        channel-priority: strict
+        environment-file: ${{ env.ENV_FILE }}
+        use-only-tar-bz2: true
+
+    - name: Build Pandas
+      uses: ./.github/actions/build_pandas
 
     - name: Linting
-      run: |
-        source activate pandas-dev
-        ci/code_checks.sh lint
+      run: ci/code_checks.sh lint
       if: always()
 
     - name: Checks on imported code
-      run: |
-        source activate pandas-dev
-        ci/code_checks.sh code
+      run: ci/code_checks.sh code
       if: always()
 
     - name: Running doctests
-      run: |
-        source activate pandas-dev
-        ci/code_checks.sh doctests
+      run: ci/code_checks.sh doctests
       if: always()
 
     - name: Docstring validation
-      run: |
-        source activate pandas-dev
-        ci/code_checks.sh docstrings
+      run: ci/code_checks.sh docstrings
       if: always()
 
     - name: Typing validation
-      run: |
-        source activate pandas-dev
-        ci/code_checks.sh typing
+      run: ci/code_checks.sh typing
       if: always()
 
     - name: Testing docstring validation script
-      run: |
-        source activate pandas-dev
-        pytest --capture=no --strict-markers scripts
+      run: pytest --capture=no --strict-markers scripts
       if: always()
 
     - name: Running benchmarks
       run: |
-        source activate pandas-dev
         cd asv_bench
         asv check -E existing
         git remote add upstream https://github.com/pandas-dev/pandas.git
@@ -93,20 +93,16 @@ jobs:
     runs-on: ubuntu-latest
     steps:
 
-    - name: Setting conda path
-      run: echo "${HOME}/miniconda3/bin" >> $GITHUB_PATH
-
     - name: Checkout
       uses: actions/checkout@v1
 
-    - name: Setup environment and build pandas
-      run: ci/setup_env.sh
+    - name: Set up pandas
+      uses: ./.github/actions/setup
 
     - name: Build website
       run: |
         source activate pandas-dev
         python web/pandas_web.py web/pandas --target-path=web/build
-
     - name: Build documentation
       run: |
         source activate pandas-dev
@@ -132,3 +128,66 @@ jobs:
     - name: Upload dev docs
       run: rsync -az --delete doc/build/html/ docs@${{ secrets.server_ip }}:/usr/share/nginx/pandas/pandas-docs/dev
       if: github.event_name == 'push'
+
+    - name: Move docs into site directory
+      run: mv doc/build/html web/build/docs
+    - name: Save website as an artifact
+      uses: actions/upload-artifact@v2
+      with:
+        name: website
+        path: web/build
+        retention-days: 14
+
+  data_manager:
+    name: Test experimental data manager
+    runs-on: ubuntu-latest
+    steps:
+
+    - name: Checkout
+      uses: actions/checkout@v1
+
+    - name: Set up pandas
+      uses: ./.github/actions/setup
+
+    - name: Run tests
+      env:
+        PANDAS_DATA_MANAGER: array
+      run: |
+        source activate pandas-dev
+
+        pytest pandas/tests/frame/
+        pytest pandas/tests/reductions/
+        pytest pandas/tests/generic/test_generic.py
+        pytest pandas/tests/arithmetic/
+        pytest pandas/tests/groupby/
+        pytest pandas/tests/resample/
+        pytest pandas/tests/reshape/merge
+        pytest pandas/tests/series/
+
+        # indexing subset (temporary since other tests don't pass yet)
+        pytest pandas/tests/indexing/multiindex/test_setitem.py::TestMultiIndexSetItem::test_astype_assignment_with_dups
+        pytest pandas/tests/indexing/multiindex/test_setitem.py::TestMultiIndexSetItem::test_frame_setitem_multi_column
+
+        pytest pandas/tests/api/
+        pytest pandas/tests/arrays/
+        pytest pandas/tests/base/
+        pytest pandas/tests/computation/
+        pytest pandas/tests/config/
+        pytest pandas/tests/dtypes/
+        pytest pandas/tests/generic/
+        pytest pandas/tests/indexes/
+        pytest pandas/tests/io/test_* -m "not slow and not clipboard"
+        pytest pandas/tests/io/excel/ -m "not slow and not clipboard"
+        pytest pandas/tests/io/formats/ -m "not slow and not clipboard"
+        pytest pandas/tests/io/parser/ -m "not slow and not clipboard"
+        pytest pandas/tests/io/sas/ -m "not slow and not clipboard"
+        pytest pandas/tests/io/xml/ -m "not slow and not clipboard"
+        pytest pandas/tests/libs/
+        pytest pandas/tests/plotting/
+        pytest pandas/tests/scalar/
+        pytest pandas/tests/strings/
+        pytest pandas/tests/tools/
+        pytest pandas/tests/tseries/
+        pytest pandas/tests/tslibs/
+        pytest pandas/tests/util/
+        pytest pandas/tests/window/

.github/workflows/comment_bot.yml

@@ -29,7 +29,7 @@ jobs:
       - name: Install-pre-commit
         run: python -m pip install --upgrade pre-commit
       - name: Run pre-commit
-        run: pre-commit run --all-files || (exit 0)
+        run: pre-commit run --from-ref=origin/master --to-ref=HEAD --all-files || (exit 0)
       - name: Commit results
         run: |
           git config user.name "$(git log -1 --pretty=format:%an)"

.github/workflows/database.yml

@@ -72,20 +72,16 @@ jobs:
         environment-file: ${{ env.ENV_FILE }}
         use-only-tar-bz2: true
 
-    - name: Environment Detail
-      run: |
-        conda info
-        conda list
-
     - name: Build Pandas
-      run: |
-        python setup.py build_ext -j 2
-        python -m pip install -e . --no-build-isolation --no-use-pep517
+      uses: ./.github/actions/build_pandas
 
     - name: Test
       run: ci/run_tests.sh
       if: always()
 
+    - name: Build Version
+      run: pushd /tmp && python -c "import pandas; pandas.show_versions();" && popd
+
     - name: Publish test results
       uses: actions/upload-artifact@master
       with:
@@ -155,20 +151,16 @@ jobs:
         environment-file: ${{ env.ENV_FILE }}
         use-only-tar-bz2: true
 
-    - name: Environment Detail
-      run: |
-        conda info
-        conda list
-
     - name: Build Pandas
-      run: |
-        python setup.py build_ext -j 2
-        python -m pip install -e . --no-build-isolation --no-use-pep517
+      uses: ./.github/actions/build_pandas
 
     - name: Test
       run: ci/run_tests.sh
       if: always()
 
+    - name: Build Version
+      run: pushd /tmp && python -c "import pandas; pandas.show_versions();" && popd
+
     - name: Publish test results
       uses: actions/upload-artifact@master
       with:
@@ -178,3 +170,11 @@ jobs:
 
     - name: Print skipped tests
       run: python ci/print_skipped.py
+
+    - name: Upload coverage to Codecov
+      uses: codecov/codecov-action@v1
+      with:
+        files: /tmp/test_coverage.xml
+        flags: unittests
+        name: codecov-pandas
+        fail_ci_if_error: true

.gitignore

@@ -110,7 +110,7 @@ asv_bench/pandas/
 doc/source/generated
 doc/source/user_guide/styled.xlsx
 doc/source/reference/api
-doc/source/_static
+doc/source/_static/*.html
 doc/source/vbench
 doc/source/vbench.rst
 doc/source/index.rst