QE inputs, XANES, GHAction updates. (#210)

* Image augmentation. * Augment images. * Augment images. * Specie update. * Add Latt2D, STM image (b-1) fix, image augmentation fix. * Add Latt2D, STM image (b-1) fix, image augmentation fix. * Update conf.py * Update conf.py * Multi-output graph bacthing. * Add EDOS dataset. * Temp. * Add circuit maker. * Add circuit maker. * NELECT update. * Version update, more DBs added. * Fix CHGCAR vasp. * Added volumetric reshape for CHGCAR. * Tmp * Tershoff Hamman update, specie update. * Add crop from center in STM. * Add Fourier transfor in STM. * Update STM pytest. * Add DPI to STM. * Zeo++ added, Atoms cif update, STM update, random vacancy maker added. * Atoms tempfile fix, Potcar from atoms module added. * Test for docs. * C2DB link update, docs Atoms update. * C2DB link update, docs Atoms update. * Version update, COD DB, QM9 JCTC DB added. * Compostion bug fix, elemental descriptor added. * Develop (#186) * Update outputs.py I added the calculation of the Raman intensities inside parse_raman_dat * Update outputs.py * Update outputs.py * Update outputs.py * Update cfid.py * Delete __init__.py * stylecss added. * stylecss added. * Adding extra Makefile/ * Remove examples from docs. * Docs update. * Docs update. * Docs update. * Docs update. * Docs update. * Docs update. * Docs update. * Docs update. * Docs update. * Docs update. * Tutorials update. * Tutorials docs update. * Docs update,pdb reader updated. * Update action_build.yml * Update action_build.yml * Remove pytraj strong dependencies. * Update docs, Added PDBBind and HPOV datasets. * Docs update. * Add thcikness to surface builder. * Surface builder update, Chemical only magpie descriptors added, pdb_core dataset added, zeopp tempfile bugfix. * Typo fix. * Add names to chem descs. * Lessen hermsolver pytest. * Reduced pytest. * Reduced pytest. * Reduced pytest. * Reduced pytest. * Reduced pytest. * No DFT3D * Exclude dft_3d dataset for memory issue. * Update figshare test. * Update figshare test. * Exclude db from coverage. * Exclude db from coverage. * Add magpie.json. * Add magpie.json. * Wien2k bands bug fix. * Wien2k bands bug fix. * Update JARVIS-FF,Elastictensor,LAMMPS parse folder, VASP bandstructure plot code. * JFF update. * Add JQE_TB3 and hMOF dataset. * Update LAMMPS module. * Update LAMMPS module. * Fix elastic tensor module. * Figshare update, docs db name update. * Substitutions. * Update figshare dft_3d, cfid_3d. * Docs data update. * Generate substitutions. * Lint fix. * Update DOS. * Update DOS. * Adding folders for nexus setup. * Update QMOF and hMOF info. * Fixing auto klength error. * Adding zeopp surface area. * Vacancy bug fix, added hmof to docs. * vacancy update. * QE inputs update. * Pyhon 3.9 test, added QE el-ph, VASP XANES, modified hmof db details. * Update Contribution.rst * Minor lint fix. * Update action_build.yml * Update action_build.yml * Fix qiskit requirements. * Fix phonopy requirements. * Fix all requirements. * Fix phonopy requirements. * QE test. * QE test. * Update action_build. * Try other python versions. * Try other python versions. * README updates. * Adding nexus. (#197) * Develop (#196) * Image augmentation. * Augment images. * Augment images. * Specie update. * Add Latt2D, STM image (b-1) fix, image augmentation fix. * Add Latt2D, STM image (b-1) fix, image augmentation fix. * Update conf.py * Update conf.py * Multi-output graph bacthing. * Add EDOS dataset. * Temp. * Add circuit maker. * Add circuit maker. * NELECT update. * Version update, more DBs added. * Fix CHGCAR vasp. * Added volumetric reshape for CHGCAR. * Tmp * Tershoff Hamman update, specie update. * Add crop from center in STM. * Add Fourier transfor in STM. * Update STM pytest. * Add DPI to STM. * Zeo++ added, Atoms cif update, STM update, random vacancy maker added. * Atoms tempfile fix, Potcar from atoms module added. * Test for docs. * C2DB link update, docs Atoms update. * C2DB link update, docs Atoms update. * Version update, COD DB, QM9 JCTC DB added. * Compostion bug fix, elemental descriptor added. * Develop (#186) * Update outputs.py I added the calculation of the Raman intensities inside parse_raman_dat * Update outputs.py * Update outputs.py * Update outputs.py * Update cfid.py * Delete __init__.py * stylecss added. * stylecss added. * Adding extra Makefile/ * Remove examples from docs. * Docs update. * Docs update. * Docs update. * Docs update. * Docs update. * Docs update. * Docs update. * Docs update. * Docs update. * Docs update. * Tutorials update. * Tutorials docs update. * Docs update,pdb reader updated. * Update action_build.yml * Update action_build.yml * Remove pytraj strong dependencies. * Update docs, Added PDBBind and HPOV datasets. * Docs update. * Add thcikness to surface builder. * Surface builder update, Chemical only magpie descriptors added, pdb_core dataset added, zeopp tempfile bugfix. * Typo fix. * Add names to chem descs. * Lessen hermsolver pytest. * Reduced pytest. * Reduced pytest. * Reduced pytest. * Reduced pytest. * Reduced pytest. * No DFT3D * Exclude dft_3d dataset for memory issue. * Update figshare test. * Update figshare test. * Exclude db from coverage. * Exclude db from coverage. * Add magpie.json. * Add magpie.json. * Wien2k bands bug fix. * Wien2k bands bug fix. * Update JARVIS-FF,Elastictensor,LAMMPS parse folder, VASP bandstructure plot code. * JFF update. * Add JQE_TB3 and hMOF dataset. * Update LAMMPS module. * Update LAMMPS module. * Fix elastic tensor module. * Figshare update, docs db name update. * Substitutions. * Update figshare dft_3d, cfid_3d. * Docs data update. * Generate substitutions. * Lint fix. * Update DOS. * Update DOS. Co-authored-by: tavazza <[email protected]> Co-authored-by: knc6 <[email protected]> Co-authored-by: KAMAL CHOUDHARY <[email protected]> * First input. * added black * Example folder. Co-authored-by: Kamal Choudhary <[email protected]> Co-authored-by: tavazza <[email protected]> Co-authored-by: knc6 <[email protected]> Co-authored-by: KAMAL CHOUDHARY <[email protected]> * Revert back. * Update .readthedocs.yaml * Update dev-requirements.txt * Docs requirements update. * Update .readthedocs.yaml * Update requirements.txt * Update .readthedocs.yaml * Update requirements.txt * Update .readthedocs.yaml * Update requirements.txt * Update requirements.txt * Update requirements.txt * Update requirements.txt * Update requirements.txt * Update atoms.py * Fixe pbc in ase_to_Atoms. Co-authored-by: tavazza <[email protected]> Co-authored-by: knc6 <[email protected]> Co-authored-by: KAMAL CHOUDHARY <[email protected]> Co-authored-by: wines1 <[email protected]>
usnistgov · Dec 20, 2021 · d8e449f · d8e449f
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diff --git a/.github/workflows/action_build.yml b/.github/workflows/action_build.yml
@@ -7,13 +7,15 @@ jobs:
   checks:
     name: Checks
     runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: [3.8,3.9]
     steps:
     - uses: actions/checkout@v2
-
-    - name: Setup Python
-      uses: actions/setup-python@v1
+    - name: Setup Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v2
       with:
-        python-version: 3.8
+        python-version: ${{ matrix.python-version }}
 
     - uses: actions/cache@v2
       with:
@@ -36,7 +38,7 @@ jobs:
 
 
         coverage run -m pytest
-        coverage report -m
+        coverage report -m -i
         codecov
         codecov --token="b61081a0-39de-44a8-8a9c-97d4be82af6d"
         # git clone https://github.com/QEF/q-e.git

diff --git a/.readthedocs.yaml b/.readthedocs.yaml
@@ -1,7 +1,7 @@
 version: 2
 
 python:
-  version: 3.7
+  version: 3.8
   install:
     - requirements: docs/requirements.txt
     - method: pip

diff --git a/Contribution.rst b/Contribution.rst
@@ -0,0 +1,43 @@
+How to contribute
+----------------------------------------
+
+If you are new to GitHub, please look into some general guidelines on how to contribute to GitHub projects:
+
+.. image:: https://img.shields.io/badge/PRs-welcome-brightgreen.svg?style=flat-square
+        :target: http://makeapullrequest.com
+
+Some common steps are:
+
+- Fork the repository
+
+- git clone YOUR_FORKED_REPOSITORY 
+
+- Add/modify your modules/scripts etc. in the repo
+
+- Go to your forked repo's Actions tab on the webpage, enable actions which performs several automated checks
+
+- pip install black pycodestyle flake8 pydocstyle
+
+- black -l 79 YOUR_MODIFIED_SCRIPT.py 
+
+- At the jarvis folder level, run the following commands. You can also run these for individual python scripts::
+
+
+      pycodestyle --ignore E203,W503 --exclude=examples,testfiles jarvis
+      flake8 --ignore E203,W503 --exclude=examples,tests --statistics --count --exit-zero 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
+
+
+- After fixing the errors in the above step::
+
+
+      git add YOUR_MODIFIED_SCRIPT.py  
+      git commit -m 'Modified xyz.py for xyz.'
+      git push origin master (or main depending on your repo)
+
+
+- After the above steps, you can send a pull request (PR) from your forked repo to the main repo's develop branch. DO NOT submit the PR to main pr master branch.
+
+-After reviewing the PR, the admin will either merge the PR or give you feedback.
+
+
diff --git a/Installation.rst b/Installation.rst
diff --git a/README.rst b/README.rst
@@ -78,13 +78,33 @@ Capabilities
 Installation
 ---------------
 
->>> pip install -U jarvis-tools
+- We recommend installing miniconda environment from https://conda.io/miniconda.html ::
 
-or
+      bash Miniconda3-latest-Linux-x86_64.sh (for linux)
+      bash Miniconda3-latest-MacOSX-x86_64.sh (for Mac)
+      Download 32/64 bit python 3.8 miniconda exe and install (for windows)
+      Now, let's make a conda environment just for JARVIS::
+      conda create --name my_jarvis python=3.8
+      source activate my_jarvis
 
->>> conda install -c conda-forge jarvis-tools
+- Method-1: Installation using pip::
 
-For detailed instructions, please see `Installation instructions <https://github.com/usnistgov/jarvis/blob/master/Installation.rst>`__
+      pip install -U jarvis-tools
+
+- Method-2: Installation using conda::
+
+      conda install -c conda-forge jarvis-tools
+
+- Method-3: Installation using setup.py::
+
+      pip install numpy scipy matplotlib
+      git clone https://github.com/usnistgov/jarvis.git
+      cd jarvis
+      python setup.py install
+
+- Note on installing additional dependencies for all modules to function::
+
+      pip install -r dev-requirements.txt
 
 
 Example function
@@ -101,7 +121,7 @@ Example function
 >>> from jarvis.db.figshare import data
 >>> dft_3d = data(dataset='dft_3d')
 >>> print (len(dft_3d))
-48527
+55723
 >>> from jarvis.io.vasp.inputs import Poscar
 >>> for i in dft_3d:
 ...     atoms = Atoms.from_dict(i['atoms'])
@@ -111,7 +131,7 @@ Example function
 ...     poscar.write_file(filename)
 >>> dft_2d = data(dataset='dft_2d')
 >>> print (len(dft_2d))
-1070
+1079
 >>> for i in dft_2d:
 ...     atoms = Atoms.from_dict(i['atoms'])
 ...     poscar = Poscar(atoms)
@@ -151,7 +171,7 @@ Example function
 
 Find more examples at
 
-      1) https://jarvis-materials-design.github.io/dbdocs/tutorials
+      1) https://jarvis-tools.readthedocs.io/en/master/tutorials.html 
 
       2) https://github.com/JARVIS-Materials-Design/jarvis-tools-notebooks
 
@@ -171,8 +191,15 @@ https://www.nature.com/articles/s41524-020-00440-1
 References
 -----------------
 
-Please see `Publications related to JARVIS-Tools <https://jarvis-materials-design.github.io/dbdocs/publications/>`__
+Please see `Publications related to JARVIS-Tools <https://jarvis-tools.readthedocs.io/en/master/publications.html>`__
+
+How to contribute
+-----------------
+
+.. image:: https://img.shields.io/badge/PRs-welcome-brightgreen.svg?style=flat-square
+        :target: http://makeapullrequest.com
 
+For detailed instructions, please see `Contribution instructions <https://github.com/usnistgov/jarvis/blob/master/Contribution.rst>`__
 
 Correspondence
 --------------------

diff --git a/dev-requirements.txt b/dev-requirements.txt
@@ -1,32 +1,151 @@
 wheel
-qiskit >= 0.24.0
-ase>=3.21.1
-numpy>=1.18.5
-scipy>=1.4.1
-matplotlib>=3.0.0
-phonopy==2.10.0
-coverage>=5.5
-lightgbm>=2.1.0
-flask >=1.1.2
-joblib >=1.0.1
-networkx >=2.5
-scikit-learn >=0.24.1
-pandas >=1.2.3
-dgl>=0.6.0.post1
-tqdm>=4.59.0
-pennylane==0.14.1
-codecov >=2.1.11
-torch >=1.8.0
-keras >=2.4.3
-tensorflow>=2.4.0
+setuptools
+absl-py==1.0.0
+alabaster==0.7.12
+appdirs==1.4.4
+ase==3.22.1
+astunparse==1.6.3
+attrs==21.2.0
+autograd==1.3
+Babel==2.9.1
+bokeh==2.4.2
+cachetools==4.2.4
+certifi==2021.10.8
+cffi==1.15.0
+charset-normalizer==2.0.9
 cif2cell==2.0.0a3
+click==8.0.3
+codecov==2.1.12
+coverage==6.2
+cryptography==36.0.1
+cycler==0.11.0
+dgl==0.6.1
+dill==0.3.4
+dlx==1.0.4
+docplex==2.22.213
+docutils==0.17.1
+execnet==1.9.0
+fastdtw==0.3.4
+fastjsonschema==2.15.2
+Flask==2.0.2
+flatbuffers==2.0
+fonttools==4.28.5
+future==0.18.2
+gast==0.4.0
+google-auth==2.3.3
+google-auth-oauthlib==0.4.6
+google-pasta==0.2.0
+grpcio==1.43.0
+h5py==3.2.1
+idna==3.3
+imageio==2.13.3
+imagesize==1.3.0
+importlib-metadata==4.9.0
+importlib-resources==5.4.0
+inflection==0.5.1
+iniconfig==1.1.1
+itsdangerous==2.0.1
+Jinja2==3.0.3
+joblib==1.1.0
+jsonschema==4.3.1
+julia==0.5.6
+keras==2.7.0
+Keras-Preprocessing==1.1.2
+kiwisolver==1.3.2
+libclang==12.0.0
+lightgbm==3.3.1
+lxml==4.7.1
+Markdown==3.3.6
+MarkupSafe==2.0.1
+matplotlib==3.5.1
+more-itertools==8.12.0
+mpmath==1.2.1
+multitasking==0.0.10
+networkx==2.6.3
+ntlm-auth==1.5.0
+numpy==1.20.0
+oauthlib==3.1.1
+opencv-python==4.5.4.60
+opt-einsum==3.3.0
+packaging==21.3
+pandas==1.3.5
+pbr==5.8.0
+PennyLane==0.14.1
+phonopy==2.10.0
+Pillow==8.4.0
+pluggy==1.0.0
+ply==3.11
+protobuf==3.19.1
+psutil==5.8.0
+py==1.11.0
+pyasn1==0.4.8
+pyasn1-modules==0.2.8
+pybind11==2.8.1
 PyCifRW==4.4
-pytest >=6.2.2
-pytest-cov >=2.11.1
-pytest-xdist>=2.2.1
-bokeh>=2.3.0
-opencv-python>=4.5.2.52
-scikit-image>=0.16.2
-Pillow>=7.1.2
-sphinx_rtd_theme>=0.5.1
-sphinx>=4.0.3
+pycparser==2.21
+Pygments==2.10.0
+pyparsing==3.0.6
+pyrsistent==0.18.0
+pytest==6.2.5
+pytest-cov==3.0.0
+pytest-forked==1.4.0
+pytest-xdist==2.5.0
+python-constraint==1.4.0
+python-dateutil==2.8.2
+pytz==2021.3
+PyWavelets==1.2.0
+PyYAML==6.0
+qiskit==0.30.1
+qiskit-aer==0.9.0
+qiskit-aqua==0.9.5
+qiskit-ibmq-provider==0.16.0
+qiskit-ignis==0.6.0
+qiskit-terra==0.18.3
+Quandl==3.7.0
+requests==2.26.0
+requests-ntlm==1.1.0
+requests-oauthlib==1.3.0
+retworkx==0.10.2
+rsa==4.8
+scikit-image==0.19.1
+scikit-learn==1.0.1
+scipy==1.8.0rc1
+semantic-version==2.6.0
+six==1.16.0
+snowballstemmer==2.2.0
+spglib==1.16.3
+Sphinx==4.3.2
+sphinx-rtd-theme==1.0.0
+sphinxcontrib-applehelp==1.0.2
+sphinxcontrib-devhelp==1.0.2
+sphinxcontrib-htmlhelp==2.0.0
+sphinxcontrib-jsmath==1.0.1
+sphinxcontrib-qthelp==1.0.3
+sphinxcontrib-serializinghtml==1.1.5
+stevedore==3.5.0
+symengine==0.8.1
+sympy==1.9
+tensorboard==2.7.0
+tensorboard-data-server==0.6.1
+tensorboard-plugin-wit==1.8.0
+tensorflow==2.7.0
+tensorflow-estimator==2.7.0
+tensorflow-io-gcs-filesystem==0.23.1
+termcolor==1.1.0
+threadpoolctl==3.0.0
+tifffile==2021.11.2
+toml==0.10.2
+tomli==2.0.0
+toolz==0.11.2
+torch==1.10.1
+tornado==6.1
+tqdm==4.62.3
+tweedledum==1.1.1
+typing_extensions==4.0.1
+urllib3==1.26.7
+websocket-client==1.2.3
+Werkzeug==2.0.2
+wrapt==1.13.3
+xmltodict==0.12.0
+yfinance==0.1.67
+zipp==3.6.0