Merge pull request #310 from Urban-Analytics/Mollys_DA

Merge Mollys DA branch ready for journal paper submission

.github/issue-branch.yml

@@ -1,2 +1,2 @@
-# this is a config file for the issue-branch action
-branchName: '${assignee.login}-issue-${issue.number}' 
+# this is a config file for the issue-branch action
+branchName: '${assignee.login}-issue-${issue.number}' 

.github/workflows/deploy-docs.yml

@@ -1,34 +1,34 @@
-name: "build documentation and deploy to gh-pages"
-on:
-  push:
-    branches:
-    - master
-
-jobs:
-  docs:
-    runs-on: ubuntu-latest
-    steps:
-    - uses: actions/checkout@v2
-    - uses: conda-incubator/setup-miniconda@v2
-      with:
-        activate-environment: ramp-ua
-        environment-file: environment.yml
-        auto-activate-base: false
-
-    - name: make docs
-      shell: bash -l {0}
-      run: |
-        conda activate ramp-ua
-        python setup.py install
-        cd docs
-        make clean
-        make html
-        touch build/html/.nojekyll
-
-    - name: deploy
-      uses: JamesIves/[email protected]
-      with:
-        BRANCH: gh-pages
-        FOLDER: docs/build/html
-        github_token: ${{ secrets.GITHUB_TOKEN }}
-        CLEAN: true
+name: "build documentation and deploy to gh-pages"
+on:
+  push:
+    branches:
+    - master
+
+jobs:
+  docs:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v2
+    - uses: conda-incubator/setup-miniconda@v2
+      with:
+        activate-environment: ramp-ua
+        environment-file: environment.yml
+        auto-activate-base: false
+
+    - name: make docs
+      shell: bash -l {0}
+      run: |
+        conda activate ramp-ua
+        python setup.py install
+        cd docs
+        make clean
+        make html
+        touch build/html/.nojekyll
+
+    - name: deploy
+      uses: JamesIves/[email protected]
+      with:
+        BRANCH: gh-pages
+        FOLDER: docs/build/html
+        github_token: ${{ secrets.GITHUB_TOKEN }}
+        CLEAN: true

.github/workflows/issue-branch.yml

@@ -1,16 +1,16 @@
-on:
-    issues:
-        types: [assigned]
-    issue_comment:
-        types: [created]
-    pull_request:
-        types: [closed]
-
-jobs:
-    create_issue_branch_job:
-        runs-on: ubuntu-latest
-        steps:
-        - name: Create Issue Branch
-          uses: robvanderleek/create-issue-branch@master
-          env:
-            GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+on:
+    issues:
+        types: [assigned]
+    issue_comment:
+        types: [created]
+    pull_request:
+        types: [closed]
+
+jobs:
+    create_issue_branch_job:
+        runs-on: ubuntu-latest
+        steps:
+        - name: Create Issue Branch
+          uses: robvanderleek/create-issue-branch@master
+          env:
+            GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/pythontesting.yml

@@ -1,59 +1,59 @@
-
-name: python-testing
-
-# Only run this for pushes to master, develop-AC and for pull requests to master
-on:
-  push:
-    branches:
-    - master
-    - develop-AC
-  pull_request:
-    branches:
-    - master
-
-# This job installs dependencies, build the book, and pushes it to `gh-pages`
-jobs:
-  pytest:
-    runs-on: ${{ matrix.os }}
-
-    name: ${{ matrix.os }}
-
-    strategy:
-      matrix:
-        os: ["ubuntu-latest", "macos-latest"] # dropping windows-latest from test matrix due to issues with rpy2 issue #73
-
-    steps:
-    - uses: actions/checkout@v2
-    - uses: conda-incubator/setup-miniconda@v2
-      with:
-        environment-file: environment.yml
-        auto-activate-base: false
-        activate-environment: ramp-ua
-
-    - name: install rampuaR
-      shell: bash -l {0}
-      run: |
-        R -e "devtools::install_github('Urban-Analytics/rampuaR', dependencies = F);"
-
-    - name: run setup.py
-      shell: bash -l {0}
-      run: |
-        conda activate ramp-ua
-        python setup.py install
-
-    - name: install pytest-cov
-      shell: bash -l {0}
-      run: |
-        conda activate ramp-ua
-        pip install pytest-cov
-
-    # run pytest within conda environment
-    - name: Run pytest and generate coverage report
-      shell: bash -l {0}
-      run: |
-        conda activate ramp-ua
-        pytest --cov=microsim tests/ --cov-report=xml
-    - name: Upload coverage report to codecov
-      uses: codecov/codecov-action@v1
-      with:
-        file: ./coverage.xml
+
+name: python-testing
+
+# Only run this for pushes to master, develop-AC and for pull requests to master
+on:
+  push:
+    branches:
+    - master
+    - develop-AC
+  pull_request:
+    branches:
+    - master
+
+# This job installs dependencies, build the book, and pushes it to `gh-pages`
+jobs:
+  pytest:
+    runs-on: ${{ matrix.os }}
+
+    name: ${{ matrix.os }}
+
+    strategy:
+      matrix:
+        os: ["ubuntu-latest", "macos-latest"] # dropping windows-latest from test matrix due to issues with rpy2 issue #73
+
+    steps:
+    - uses: actions/checkout@v2
+    - uses: conda-incubator/setup-miniconda@v2
+      with:
+        environment-file: environment.yml
+        auto-activate-base: false
+        activate-environment: ramp-ua
+
+    - name: install rampuaR
+      shell: bash -l {0}
+      run: |
+        R -e "devtools::install_github('Urban-Analytics/rampuaR', dependencies = F);"
+
+    - name: run setup.py
+      shell: bash -l {0}
+      run: |
+        conda activate ramp-ua
+        python setup.py install
+
+    - name: install pytest-cov
+      shell: bash -l {0}
+      run: |
+        conda activate ramp-ua
+        pip install pytest-cov
+
+    # run pytest within conda environment
+    - name: Run pytest and generate coverage report
+      shell: bash -l {0}
+      run: |
+        conda activate ramp-ua
+        pytest --cov=microsim tests/ --cov-report=xml
+    - name: Upload coverage report to codecov
+      uses: codecov/codecov-action@v1
+      with:
+        file: ./coverage.xml

.github/workflows/tagged-release.yml

@@ -1,45 +1,45 @@
-# this action automates the process of creating a github release
-#
-# you can prompt this action by creating a git tag that follows semantic versioning (https://semver.org/) major.minor.patch
-# e.g. in command line: git tag -a v0.1.2 -m 'tag comment about tag'
-# you'll then need to do `git push --tags` to push the tag refs to github
-# this action will then run
-
-name: "tagged-release"
-
-on:
-  push:
-    tags:
-      - v*
-
-jobs:
-  tagged-release:
-    name: "Tagged Release"
-    runs-on: "ubuntu-latest"
-
-    steps:
-      - uses: actions/checkout@v2
-      - uses: conda-incubator/setup-miniconda@v2
-        with:
-          environment-file: environment.yml
-          auto-activate-base: false
-          activate-environment: ramp-ua
-
-      - name: install package and test
-        shell: bash -l {0}
-        run: |
-          python setup.py install 
-          pytest
-          echo "Tests complete"
-
-      - name: create sdist
-        shell: bash -l {0}
-        run: |
-          python setup.py sdist
-
-      - uses: "marvinpinto/action-automatic-releases@latest"
-        with:
-          repo_token: "${{ secrets.GITHUB_TOKEN }}"
-          prerelease: false
-          files: |
+# this action automates the process of creating a github release
+#
+# you can prompt this action by creating a git tag that follows semantic versioning (https://semver.org/) major.minor.patch
+# e.g. in command line: git tag -a v0.1.2 -m 'tag comment about tag'
+# you'll then need to do `git push --tags` to push the tag refs to github
+# this action will then run
+
+name: "tagged-release"
+
+on:
+  push:
+    tags:
+      - v*
+
+jobs:
+  tagged-release:
+    name: "Tagged Release"
+    runs-on: "ubuntu-latest"
+
+    steps:
+      - uses: actions/checkout@v2
+      - uses: conda-incubator/setup-miniconda@v2
+        with:
+          environment-file: environment.yml
+          auto-activate-base: false
+          activate-environment: ramp-ua
+
+      - name: install package and test
+        shell: bash -l {0}
+        run: |
+          python setup.py install 
+          pytest
+          echo "Tests complete"
+
+      - name: create sdist
+        shell: bash -l {0}
+        run: |
+          python setup.py sdist
+
+      - uses: "marvinpinto/action-automatic-releases@latest"
+        with:
+          repo_token: "${{ secrets.GITHUB_TOKEN }}"
+          prerelease: false
+          files: |
             dist/*.tar.gz

.gitignore

@@ -31,7 +31,7 @@ __pycache__
 
 # snapshot files
 *.npz
-*.pkl
+#*.pkl
 
 # setuptools items
 **/*.egg-info/*