Merge pull request #154 from alchemistry/prepare-050

prepare for release 0.5.0
alchemistry · Aug 1, 2021 · b068776 · b068776
2 parents eaafdb3 + ff7ed5d
commit b068776
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diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
@@ -11,19 +11,18 @@ on:
     branches:
       - "master"
 
+concurrency:
+  group: "${{ github.ref }}-${{ github.head_ref }}"
+  cancel-in-progress: true
+
 jobs:
   test:
     runs-on: ${{ matrix.os }}
     strategy:
-      fail-fast: false
+      fail-fast: true
       matrix:
-        os: 
-          - ubuntu-latest
-         #- macOS-latest 
-        python-version: 
-          - 3.7
-          - 3.8
-          - 3.9
+        os: ["ubuntu-latest", "macOS-latest", "windows-latest"]
+        python-version: ["3.7", "3.8", "3.9"]   
 
     steps:
     - uses: actions/checkout@v2
@@ -32,36 +31,36 @@ jobs:
       uses: actions/setup-python@v2
       with:
         python-version: ${{ matrix.python-version }}
-        architecture: x64
 
-    - name: Environment Information
-      shell: bash -l {0}
+    - name: Display Python version
+      run: python -c "import sys; print(sys.version)"
+
+    - name: Install some dependencies (binary only, no version restrictions)
       run: |
-        python --version
+        python -m pip install wheel
+        python -m pip install --only-binary=numpy numpy
+        python -m pip install --only-binary=scipy scipy
+        python -m pip install --only-binary=matplotlib matplotlib
 
     - name: Install pytest, pytest plugins
-      shell: bash -l {0}
       run: |
         python -m pip install pytest pytest-cov pytest-pep8
 
     - name: Install alchemtest
-      shell: bash -l {0}
       run: |
-        python -m pip install --only-binary=numpy numpy # Otherwise this would take ages
         python -m pip install https://github.com/alchemistry/alchemtest/archive/master.zip
 
-    - name: Install package
-      shell: bash -l {0}
+    - name: Install package (with remaining dependencis)
       run: |
         python -m pip install .
 
     - name: Run tests
-      shell: bash -l {0}
       run: |
-        pytest -v --cov alchemlyb --cov-report=xml src/alchemlyb/tests
+        pytest -v --cov alchemlyb --cov-report=xml --color=yes src/alchemlyb/tests
 
     - name: Codecov
       uses: codecov/[email protected]
       with:
+        name: codecov-${{ matrix.os }}-py${{ matrix.python-version }}
         file: ./coverage.xml
         fail_ci_if_error: true
diff --git a/CHANGES b/CHANGES
@@ -13,36 +13,40 @@ The rules for this file:
   * release numbers follow "Semantic Versioning" http://semver.org
 
 ------------------------------------------------------------------------------
-??/??/2021 xiki-tempula, orbeckst
+08/01/2021 xiki-tempula, orbeckst
 
   * 0.5.0
 
+Changes
+  - alchemlyb adopts NEP29
+    https://numpy.org/neps/nep-0029-deprecation_policy.html
+    to effectively only support the last 2-3 minor Python versions    
+  - Removed support for Python 2.7 and 3.6 (issue #130, #140):
+    supported/tested Python versions are 3.7, 3.8, 3.9 on
+    Linux, macOS, and Windows
+  - The scipy constant for gas constant is used for parsers instead of the
+    constants used by the corresponding MD engine (issue #125, PR #129).
+    This leads to small changes in results from GROMACS simulations in kT
+    compared to the previous releases, with a relative difference on the order
+    of 1e-7.    
+  - Added unit-awareness: the base unit remains kT but dataframes need to
+    carry the unit and temperature in a DataFrame.attrs so that dataframes
+    can be easily converted to different energy units (issue #125)
+  - The parser outputs dataframe with metadata (issue #125, PR #129).    
+  - Visualisation module will change the data according to input unit
+    (issue #125, PR #129).
+  - Bump the minimum pandas version to 1.2 (issue #130, #140).
+
 Enhancements
   - postprocessors.units module for unit conversion (issue #125, PR #129).
   - pass_attrs decorator for safely passing variable (issue #125, PR #129).
   - alchemlyb.concat added to replace pd.concat (issue #125, PR #129).
 
-Deprecations
-
 Fixes
-  - `alchemlyb.concat()` should raise ValueError when given empty list, to be compatible with
-    pandas.concat() (issue #150, PR #152).
-  - Fix the support for pandas >= 1.3 (issue #147, PR #148).
+  - `alchemlyb.concat()` should raise ValueError when given empty list, to be
+    compatible with pandas.concat() (issue #150, PR #152).
+  - Fix the support for pandas >= 1.3 by skipping 1.3.0 (issue #147, PR #148).
   - Fix separate_dhdl not work for multiple columns (issue #149, PR #151).
-
-Changes
-  - The scipy constant for gas constant is used for parsers instead of the
-    constants used by the corresponding MD engine (issue #125, PR #129).
-    This leads to small changes in results from GROMACS simulations compared to the 
-    previous releases.
-  - Visualisation module will change the data according to input unit (issue
-  #125,PR #129).
-  - The parser output dataframe with metadata (issue #125, PR #129).
-  - alchemlyb adopts NEP29
-    https://numpy.org/neps/nep-0029-deprecation_policy.html
-    to effectively only support the last 2-3 minor Python versions
-  - Removed support for Python 2.7 and 3.6 (issue #130, #140).
-  - Bump the minimum pandas version to 1.2 (issue #130, #140).
 
 
 06/08/2021 orbeckst

diff --git a/setup.py b/setup.py
@@ -43,5 +43,6 @@
       long_description=open('README.rst').read(),
       long_description_content_type='text/x-rst',
       tests_require = ['pytest', 'alchemtest'],
-      install_requires=['numpy', 'pandas>=1.2,!=1.3.0', 'pymbar>=3.0.5,<4', 'scipy', 'scikit-learn', 'matplotlib']
+      install_requires=['numpy', 'pandas>=1.2,!=1.3.0', 'pymbar>=3.0.5,<4',
+                        'scipy', 'scikit-learn', 'matplotlib']
       )