improvement: add Atoms.clone() and remove sites by indices, including in-place

.github/workflows/action_build.yml

@@ -1,58 +1,116 @@
 name: JARVIS-Tools github action
-
 on: [push, pull_request]
 
 jobs:
-  checks:
-    name: Checks
-    runs-on: ubuntu-latest
+  miniconda:
+    name: Miniconda ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
     strategy:
-      matrix:
-        python-version: ["3.9","3.10"]
+        matrix:
+            os: ["ubuntu-latest"]
     steps:
-    - uses: actions/checkout@v2
-    - name: Setup Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
-      with:
-        python-version: ${{ matrix.python-version }}
-
-    - uses: actions/cache@v2
-      with:
-        path: ${{ env.pythonLocation }}
-        key: ${{ env.pythonLocation }}-${{ hashFiles('setup.py') }}-${{ hashFiles('dev-requirements.txt') }}
-
-    - name: Install requirements
-      run: |
-        pip install --upgrade pip
-        pip install pycodestyle flake8 pydocstyle 
-        flake8 --ignore E203,W503 --exclude=examples,tests --statistics --count --exit-zero jarvis
-        pycodestyle --ignore E203,W503 --exclude=examples,testfiles jarvis
-        pydocstyle --match-dir=core --match-dir=io --match-dir=io --match-dir=ai --match-dir=analysis --match-dir=db --match-dir=tasks --count jarvis
+      - uses: actions/checkout@v2
+      - uses: conda-incubator/setup-miniconda@v2
+        with:
+          activate-environment: test
+          environment-file: environment.yml
+          python-version: "3.10"
+          auto-activate-base: false
+      - shell: bash -l {0}
+        run: |
+          conda info
+          conda list
+      - name: Lint
+        shell: bash -l {0}
+        run: |
+            conda install flake8 pycodestyle pydocstyle
+            flake8 --ignore E203,W503 --exclude=examples,tests --statistics --count --exit-zero jarvis
+            pycodestyle --ignore E203,W503 --exclude=examples,testfiles jarvis
+            pydocstyle --match-dir=core --match-dir=io --match-dir=io --match-dir=ai --match-dir=analysis --match-dir=db --match-dir=tasks --count jarvis
+
+      - name: Run pytest
+        shell: bash -l {0}
+        run: |
+            conda install pytest coverage codecov
+            python setup.py develop
+            coverage run -m pytest
+            coverage report -m -i
+            codecov
+            codecov --token="b61081a0-39de-44a8-8a9c-97d4be82af6d"
+            rm POSCAR* *.png
+
+
+
+
+# name: JARVIS-Tools github action
+
+# on: [push, pull_request]
+
+# jobs:
+#   checks:
+#     name: Checks
+#     runs-on: ubuntu-latest
+#     defaults:
+#       run:
+#         shell: bash -l {0}
+#     strategy:
+#       matrix:
+#         python-version: ["3.10"]
+#     steps:
+#     - uses: actions/checkout@v2
+#     - name: Setup Python ${{ matrix.python-version }}
+#       uses: actions/setup-python@v2
+#       with:
+#         python-version: ${{ matrix.python-version }}
+
+#     - uses: actions/cache@v2
+#       with:
+#         path: ${{ env.pythonLocation }}
+#         key: ${{ env.pythonLocation }}-${{ hashFiles('setup.py') }}-${{ hashFiles('dev-requirements.txt') }}
+
+#     - name: Install requirements
+#       run: |
+#         source ~/.bashrc
+#         echo "begin: PATH=$PATH;"
+#         find . -type f > before_test_files.txt
+#         conda env create -f environment.yml
+#         conda activate my_jarvis
+#         conda install pandas numpy matplotlib phonopy scikit-learn --quiet
+#         pip install --upgrade pip
+#         pip install pycodestyle flake8 pydocstyle coverage pytest codecov qiskit==0.41.1
+#         flake8 --ignore E203,W503 --exclude=examples,tests --statistics --count --exit-zero jarvis
+#         pycodestyle --ignore E203,W503 --exclude=examples,testfiles jarvis
+#         pydocstyle --match-dir=core --match-dir=io --match-dir=io --match-dir=ai --match-dir=analysis --match-dir=db --match-dir=tasks --count jarvis
+
+#         #python setup.py develop
+#         #pip install --upgrade --upgrade-strategy eager -r dev-requirements.txt -e .
+#         #conda install -c ambermd pytraj
+#         #pip install numpy scipy matplotlib
+#         #pip install -r dev-requirements.txt
 
-        #python setup.py develop
-        #pip install --upgrade --upgrade-strategy eager -r dev-requirements.txt -e .
-        #conda install -c ambermd pytraj
-        pip install numpy scipy matplotlib
-        pip install -r dev-requirements.txt
-        pip install -e .
-        echo 'CONDA LIST'
-        conda list
-
-        echo 'PIP FREEZE'
-        pip freeze
-
-        #echo 'PYTEST-COV'
-        #pytest --cov-config=.coveragerc --cov=jarvis -n 2
-
-
-        coverage run -m pytest
-        coverage report -m -i
-        codecov
-        codecov --token="b61081a0-39de-44a8-8a9c-97d4be82af6d"
-        # git clone https://github.com/QEF/q-e.git
-        # cd q-e
-        # ./configure
-        # make pw
+#         pip install -e .
+#         echo 'CONDA LIST'
+#         conda list
+
+#         echo 'PIP FREEZE'
+#         pip freeze
+
+#         #echo 'PYTEST-COV'
+#         #pytest --cov-config=.coveragerc --cov=jarvis -n 2
+
+#         coverage run -m pytest
+#         coverage report -m -i
+#         codecov
+#         codecov --token="b61081a0-39de-44a8-8a9c-97d4be82af6d"
+#         find . -type f > after_test_files.txt
+#         #comm -13 <(sort before_test_files.txt) <(sort after_test_files.txt) > new_files.txt
+#         #cat new_files.txt | xargs rm
+#         #rm before_test_files.txt after_test_files.txt new_files.txt
+
+#         # git clone https://github.com/QEF/q-e.git
+#         # cd q-e
+#         # ./configure
+#         # make pw
 
 # jobs:
 #   checks:
@@ -149,4 +207,4 @@ jobs:
 #             # git clone https://github.com/QEF/q-e.git
 #             # cd q-e
 #             # ./configure
-#             # make pw
+#             # make pw

.github/workflows/deploy_nist_pages.yml

@@ -36,40 +36,48 @@ permissions:
 #     #- '**'
 
 jobs:
-  build:
-    runs-on: ubuntu-latest
+  miniconda:
+    name: Miniconda ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+        matrix:
+            os: ["ubuntu-latest"]
     steps:
-    - uses: actions/checkout@v3
-    - name: Set up Python 3.9
-      uses: actions/setup-python@v4
-      with:
-        python-version: 3.9
-    - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip setuptools
-        python setup.py develop
-        #python -m pip install -r requirements.txt
-
-    - name: Deploy Files
-      run: |
-        git config user.name "github-actions[bot]"
-        git config user.email "[email protected]"
-        # python jarvis_leaderboard/rebuild.py
-        mkdocs build
-        #rm -r /tmp/site
-        cp -r site /tmp
-        git fetch
-        git checkout nist-pages --force
-        rm -r *
-        cp -r /tmp/site/* .
-
-        echo 'listing'
-        ls
-        echo 'listing tmp'
-        ls /tmp
-        git add * */*
-        git commit -m 'Adding files.'
-        git push origin nist-pages -f
-        #git commit -a -m "Move"
-        #git push -f origin nist-pages1
-        #mkdocs gh-deploy  
+      - uses: actions/checkout@v2
+      - uses: conda-incubator/setup-miniconda@v2
+        with:
+          activate-environment: test
+          environment-file: environment.yml
+          python-version: "3.10"
+          auto-activate-base: false
+      - shell: bash -l {0}
+        run: |
+          conda info
+          conda list
+
+      - name: Deploy Files
+        shell: bash -l {0}
+        run: |
+            python -m pip install --upgrade pip setuptools
+            python setup.py develop
+            git config user.name "github-actions[bot]"
+            git config user.email "[email protected]"
+            # python jarvis_leaderboard/rebuild.py
+            mkdocs build
+            #rm -r /tmp/site
+            cp -r site /tmp
+            git fetch
+            git checkout nist-pages --force
+            rm -r *
+            cp -r /tmp/site/* .
+
+            echo 'listing'
+            ls
+            echo 'listing tmp'
+            ls /tmp
+            git add * */*
+            git commit -m 'Adding files.'
+            git push origin nist-pages -f
+            #git commit -a -m "Move"
+            #git push -f origin nist-pages1
+            #mkdocs gh-deploy  

.gitignore

@@ -103,4 +103,8 @@ ENV/
 # mypy
 .mypy_cache/
 
-.pytest_cache/
+.pytest_cache/
+
+# pycharm
+.idea
+