Develop

.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

docs/index.md

@@ -28,9 +28,9 @@ NIST-JARVIS official website is: <https://jarvis.nist.gov> . This
 project is a part of the Materials Genome Initiative (MGI) at NIST
 (<https://mgi.nist.gov/>).
 
-For more details, checkout our latest article: [The joint automated
+For more details, checkout our latest articles: [The joint automated
 repository for various integrated simulations (JARVIS) for data-driven
-materials design](https://www.nature.com/articles/s41524-020-00440-1), [other publications](https://pages.nist.gov/jarvis/publications/) and [YouTube
+materials design](https://www.nature.com/articles/s41524-020-00440-1), [Recent progress in the JARVIS infrastructure for next-generation data-driven materials design](https://pubs.aip.org/aip/apr/article/10/4/041302/2917416), [other publications](https://pages.nist.gov/jarvis/publications/) and [YouTube
 videos](https://www.youtube.com/watch?v=P0ZcHXOC6W0&feature=emb_title&ab_channel=JARVIS-repository)
 
 
@@ -98,9 +98,9 @@ videos](https://www.youtube.com/watch?v=P0ZcHXOC6W0&feature=emb_title&ab_channel
 
         bash Miniconda3-latest-Linux-x86_64.sh (for linux)
         bash Miniconda3-latest-MacOSX-x86_64.sh (for Mac)
-        Download 32/64 bit python 3.9 miniconda exe and install (for windows)
+        Download 32/64 bit python 3.10 miniconda exe and install (for windows)
         Now, let's make a conda environment just for JARVIS::
-        conda create --name my_jarvis python=3.9
+        conda create --name my_jarvis python=3.10
         source activate my_jarvis
 
 -   Method-1: Installation using pip:
@@ -116,12 +116,19 @@ videos](https://www.youtube.com/watch?v=P0ZcHXOC6W0&feature=emb_title&ab_channel
         pip install numpy scipy matplotlib
         git clone https://github.com/usnistgov/jarvis.git
         cd jarvis
-        python setup.py install
+        python setup.py develop
 
--   Note on installing additional dependencies for all modules to
-    function:
+-   Method-4: Note on installing additional dependencies (for developers):
 
-        pip install -r dev-requirements.txt
+        conda env create --name my_jarvis -f environment.yml
+        conda activate my_jarvis
+        conda install pytest coverage codecov
+        git clone https://github.com/usnistgov/jarvis.git
+        cd jarvis
+        git checkout develop
+        python setup.py develop
+        coverage run -m pytest
+
 
 <a name="example"></a>
 ## Example function

docs/tutorials.md

@@ -643,7 +643,7 @@ import numpy as np
 from jarvis.core.composition import Composition
 from jarvis.core.specie import Specie
 from jarvis.ai.pkgs.lgbm.regression import regression
-from jarvis.ai.descriptors.cfid import get_chem_only_descriptor
+from jarvis.ai.descriptors.cfid import get_chem_only_descriptors
 
 # Load a dataset, you can use pandas read_csv also to generte my_data
 # Here is a sample dataset
@@ -671,7 +671,7 @@ X = []
 Y = []
 IDs = []
 for ii, i in enumerate(my_data):
-    X.append(get_chem_only_descriptor(i[0]))
+    X.append(get_chem_only_descriptors(i[0]))
     Y.append(i[1])
     IDs.append(ii)