Check conda

Author: knc6

.github/workflows/action_build.yml

@@ -23,17 +23,20 @@ jobs:
 
     - name: Install requirements
       run: |
+        find . -type f > before_test_files.txt
         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
-        
+                
         #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
+        conda install pandas numpy matplotlib --quiet
+        conda env create -f environment.yml
+        #pip install numpy scipy matplotlib
+        #pip install -r dev-requirements.txt
         pip install -e .
         echo 'CONDA LIST'
         conda list
@@ -49,6 +52,11 @@ jobs:
         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
@@ -149,4 +157,4 @@ jobs:
 #             # git clone https://github.com/QEF/q-e.git
 #             # cd q-e
 #             # ./configure
-#             # make pw
+#             # make pw

environment.yml

@@ -0,0 +1,274 @@
+name: my_jarvis
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - _libgcc_mutex=0.1=conda_forge
+  - _openmp_mutex=4.5=2_gnu
+  - alsa-lib=1.2.11=hd590300_1
+  - archspec=0.2.2=pyhd8ed1ab_0
+  - attr=2.5.1=h166bdaf_1
+  - boltons=23.1.1=pyhd8ed1ab_0
+  - brotli=1.1.0=hd590300_1
+  - brotli-bin=1.1.0=hd590300_1
+  - brotli-python=1.1.0=py310hc6cd4ac_1
+  - bzip2=1.0.8=hd590300_5
+  - c-ares=1.24.0=hd590300_0
+  - ca-certificates=2024.2.2=hbcca054_0
+  - cairo=1.18.0=h3faef2a_0
+  - certifi=2024.2.2=pyhd8ed1ab_0
+  - cffi=1.16.0=py310h2fee648_0
+  - charset-normalizer=3.3.2=pyhd8ed1ab_0
+  - colorama=0.4.6=pyhd8ed1ab_0
+  - conda=23.11.0=py310hff52083_1
+  - conda-libmamba-solver=23.12.0=pyhd8ed1ab_0
+  - conda-package-handling=2.2.0=pyh38be061_0
+  - conda-package-streaming=0.9.0=pyhd8ed1ab_0
+  - contourpy=1.2.0=py310hd41b1e2_0
+  - cycler=0.12.1=pyhd8ed1ab_0
+  - dbus=1.13.6=h5008d03_3
+  - distro=1.8.0=pyhd8ed1ab_0
+  - expat=2.6.2=h59595ed_0
+  - fmt=10.1.1=h00ab1b0_1
+  - font-ttf-dejavu-sans-mono=2.37=hab24e00_0
+  - font-ttf-inconsolata=3.000=h77eed37_0
+  - font-ttf-source-code-pro=2.038=h77eed37_0
+  - font-ttf-ubuntu=0.83=h77eed37_1
+  - fontconfig=2.14.2=h14ed4e7_0
+  - fonts-conda-ecosystem=1=0
+  - fonts-conda-forge=1=0
+  - fonttools=4.50.0=py310h2372a71_0
+  - freetype=2.12.1=h267a509_2
+  - gettext=0.21.1=h27087fc_0
+  - glib=2.80.0=hf2295e7_0
+  - glib-tools=2.80.0=hde27a5a_0
+  - graphite2=1.3.13=h58526e2_1001
+  - gst-plugins-base=1.22.9=h8e1006c_0
+  - gstreamer=1.22.9=h98fc4e7_0
+  - harfbuzz=8.3.0=h3d44ed6_0
+  - icu=73.2=h59595ed_0
+  - idna=3.6=pyhd8ed1ab_0
+  - jsonpatch=1.33=pyhd8ed1ab_0
+  - jsonpointer=2.4=py310hff52083_3
+  - keyutils=1.6.1=h166bdaf_0
+  - kiwisolver=1.4.5=py310hd41b1e2_1
+  - krb5=1.21.2=h659d440_0
+  - lame=3.100=h166bdaf_1003
+  - lcms2=2.16=hb7c19ff_0
+  - ld_impl_linux-64=2.40=h41732ed_0
+  - lerc=4.0.0=h27087fc_0
+  - libarchive=3.7.2=h2aa1ff5_1
+  - libblas=3.9.0=21_linux64_openblas
+  - libbrotlicommon=1.1.0=hd590300_1
+  - libbrotlidec=1.1.0=hd590300_1
+  - libbrotlienc=1.1.0=hd590300_1
+  - libcap=2.69=h0f662aa_0
+  - libcblas=3.9.0=21_linux64_openblas
+  - libclang=15.0.7=default_hb11cfb5_4
+  - libclang13=15.0.7=default_ha2b6cf4_4
+  - libcups=2.3.3=h4637d8d_4
+  - libcurl=8.5.0=hca28451_0
+  - libdeflate=1.19=hd590300_0
+  - libedit=3.1.20191231=he28a2e2_2
+  - libev=4.33=hd590300_2
+  - libevent=2.1.12=hf998b51_1
+  - libexpat=2.6.2=h59595ed_0
+  - libffi=3.4.2=h7f98852_5
+  - libflac=1.4.3=h59595ed_0
+  - libgcc-ng=13.2.0=h807b86a_3
+  - libgcrypt=1.10.3=hd590300_0
+  - libgfortran-ng=13.2.0=h69a702a_5
+  - libgfortran5=13.2.0=ha4646dd_5
+  - libglib=2.80.0=hf2295e7_0
+  - libgomp=13.2.0=h807b86a_3
+  - libgpg-error=1.48=h71f35ed_0
+  - libiconv=1.17=hd590300_2
+  - libjpeg-turbo=3.0.0=hd590300_1
+  - liblapack=3.9.0=21_linux64_openblas
+  - libllvm15=15.0.7=hb3ce162_4
+  - libmamba=1.5.5=had39da4_0
+  - libmambapy=1.5.5=py310h39ff949_0
+  - libnghttp2=1.58.0=h47da74e_1
+  - libnsl=2.0.1=hd590300_0
+  - libogg=1.3.4=h7f98852_1
+  - libopenblas=0.3.26=pthreads_h413a1c8_0
+  - libopus=1.3.1=h7f98852_1
+  - libpng=1.6.43=h2797004_0
+  - libpq=16.2=h33b98f1_1
+  - libsndfile=1.2.2=hc60ed4a_1
+  - libsolv=0.7.27=hfc55251_0
+  - libsqlite=3.44.2=h2797004_0
+  - libssh2=1.11.0=h0841786_0
+  - libstdcxx-ng=13.2.0=h7e041cc_3
+  - libsystemd0=255=h3516f8a_1
+  - libtiff=4.6.0=ha9c0a0a_2
+  - libuuid=2.38.1=h0b41bf4_0
+  - libvorbis=1.3.7=h9c3ff4c_0
+  - libwebp-base=1.3.2=hd590300_0
+  - libxcb=1.15=h0b41bf4_0
+  - libxkbcommon=1.6.0=hd429924_1
+  - libxml2=2.12.3=h232c23b_0
+  - libzlib=1.2.13=hd590300_5
+  - lz4-c=1.9.4=hcb278e6_0
+  - lzo=2.10=h516909a_1000
+  - mamba=1.5.5=py310h51d5547_0
+  - matplotlib=3.8.3=py310hff52083_0
+  - matplotlib-base=3.8.3=py310h62c0568_0
+  - menuinst=2.0.1=py310hff52083_0
+  - mpg123=1.32.4=h59595ed_0
+  - munkres=1.1.4=pyh9f0ad1d_0
+  - mysql-common=8.0.33=hf1915f5_6
+  - mysql-libs=8.0.33=hca2cd23_6
+  - ncurses=6.4=h59595ed_2
+  - nspr=4.35=h27087fc_0
+  - nss=3.97=h1d7d5a4_0
+  - openjpeg=2.5.2=h488ebb8_0
+  - openssl=3.2.1=hd590300_1
+  - packaging=23.2=pyhd8ed1ab_0
+  - pandas=2.2.1=py310hcc13569_0
+  - pcre2=10.43=hcad00b1_0
+  - pillow=10.2.0=py310h01dd4db_0
+  - pip=23.3.2=pyhd8ed1ab_0
+  - pixman=0.43.2=h59595ed_0
+  - platformdirs=4.1.0=pyhd8ed1ab_0
+  - ply=3.11=py_1
+  - pthread-stubs=0.4=h36c2ea0_1001
+  - pulseaudio-client=16.1=hb77b528_5
+  - pybind11-abi=4=hd8ed1ab_3
+  - pycosat=0.6.6=py310h2372a71_0
+  - pycparser=2.21=pyhd8ed1ab_0
+  - pyparsing=3.1.2=pyhd8ed1ab_0
+  - pyqt=5.15.9=py310h04931ad_5
+  - pyqt5-sip=12.12.2=py310hc6cd4ac_5
+  - pysocks=1.7.1=pyha2e5f31_6
+  - python=3.10.13=hd12c33a_0_cpython
+  - python-tzdata=2024.1=pyhd8ed1ab_0
+  - python_abi=3.10=4_cp310
+  - pytz=2024.1=pyhd8ed1ab_0
+  - qt-main=5.15.8=h450f30e_18
+  - readline=8.2=h8228510_1
+  - reproc=14.2.4.post0=hd590300_1
+  - reproc-cpp=14.2.4.post0=h59595ed_1
+  - ruamel.yaml=0.18.5=py310h2372a71_0
+  - ruamel.yaml.clib=0.2.7=py310h2372a71_2
+  - setuptools=68.2.2=pyhd8ed1ab_0
+  - sip=6.7.12=py310hc6cd4ac_0
+  - six=1.16.0=pyh6c4a22f_0
+  - tk=8.6.13=noxft_h4845f30_101
+  - toml=0.10.2=pyhd8ed1ab_0
+  - tomli=2.0.1=pyhd8ed1ab_0
+  - tornado=6.4=py310h2372a71_0
+  - tqdm=4.66.1=pyhd8ed1ab_0
+  - truststore=0.8.0=pyhd8ed1ab_0
+  - tzdata=2023c=h71feb2d_0
+  - unicodedata2=15.1.0=py310h2372a71_0
+  - wheel=0.42.0=pyhd8ed1ab_0
+  - xcb-util=0.4.0=hd590300_1
+  - xcb-util-image=0.4.0=h8ee46fc_1
+  - xcb-util-keysyms=0.4.0=h8ee46fc_1
+  - xcb-util-renderutil=0.3.9=hd590300_1
+  - xcb-util-wm=0.4.1=h8ee46fc_1
+  - xkeyboard-config=2.41=hd590300_0
+  - xorg-kbproto=1.0.7=h7f98852_1002
+  - xorg-libice=1.1.1=hd590300_0
+  - xorg-libsm=1.2.4=h7391055_0
+  - xorg-libx11=1.8.7=h8ee46fc_0
+  - xorg-libxau=1.0.11=hd590300_0
+  - xorg-libxdmcp=1.1.3=h7f98852_0
+  - xorg-libxext=1.3.4=h0b41bf4_2
+  - xorg-libxrender=0.9.11=hd590300_0
+  - xorg-renderproto=0.11.1=h7f98852_1002
+  - xorg-xextproto=7.3.0=h0b41bf4_1003
+  - xorg-xf86vidmodeproto=2.3.1=h7f98852_1002
+  - xorg-xproto=7.0.31=h7f98852_1007
+  - xz=5.2.6=h166bdaf_0
+  - yaml-cpp=0.8.0=h59595ed_0
+  - zlib=1.2.13=hd590300_5
+  - zstandard=0.22.0=py310h1275a96_0
+  - zstd=1.5.5=hfc55251_0
+  - pip:
+      - annotated-types==0.6.0
+      - appdirs==1.4.4
+      - autograd==1.6.2
+      - babel==2.14.0
+      - bokeh==2.4.2
+      - cif2cell==2.1.0
+      - click==8.1.7
+      - coverage==7.4.4
+      - cryptography==42.0.5
+      - dgl==2.1.0
+      - dill==0.3.8
+      - exceptiongroup==1.2.0
+      - filelock==3.13.1
+      - fsspec==2024.3.1
+      - future==1.0.0
+      - ghp-import==2.1.0
+      - h5py==3.10.0
+      - iniconfig==2.0.0
+      - jinja2==3.1.3
+      - joblib==1.3.2
+      - lightgbm==3.3.1
+      - markdown==3.6
+      - markupsafe==2.1.5
+      - mergedeep==1.3.4
+      - mkdocs==1.5.3
+      - mkdocs-material==9.5.14
+      - mkdocs-material-extensions==1.3.1
+      - mpmath==1.3.0
+      - networkx==3.2.1
+      - ntlm-auth==1.5.0
+      - numpy==1.23.5
+      - nvidia-cublas-cu12==12.1.3.1
+      - nvidia-cuda-cupti-cu12==12.1.105
+      - nvidia-cuda-nvrtc-cu12==12.1.105
+      - nvidia-cuda-runtime-cu12==12.1.105
+      - nvidia-cudnn-cu12==8.9.2.26
+      - nvidia-cufft-cu12==11.0.2.54
+      - nvidia-curand-cu12==10.3.2.106
+      - nvidia-cusolver-cu12==11.4.5.107
+      - nvidia-cusparse-cu12==12.1.0.106
+      - nvidia-nccl-cu12==2.19.3
+      - nvidia-nvjitlink-cu12==12.4.99
+      - nvidia-nvtx-cu12==12.1.105
+      - paginate==0.5.6
+      - pathspec==0.12.1
+      - pbr==6.0.0
+      - pennylane==0.14.1
+      - phonopy==2.10.0
+      - pluggy==1.4.0
+      - psutil==5.9.8
+      - pycifrw==4.4.6
+      - pydantic==2.6.4
+      - pydantic-core==2.16.3
+      - pygments==2.17.2
+      - pymdown-extensions==10.7.1
+      - pytest==8.1.1
+      - python-dateutil==2.8.2
+      - pyyaml==6.0.1
+      - pyyaml-env-tag==0.1
+      - qiskit==0.41.1
+      - qiskit-aer==0.11.2
+      - qiskit-ibmq-provider==0.20.1
+      - qiskit-terra==0.23.2
+      - regex==2023.12.25
+      - requests==2.28.2
+      - requests-ntlm==1.1.0
+      - rustworkx==0.14.2
+      - scikit-learn==1.4.1.post1
+      - scipy==1.12.0
+      - semantic-version==2.6.0
+      - spglib==2.3.1
+      - stevedore==5.2.0
+      - symengine==0.11.0
+      - sympy==1.12
+      - threadpoolctl==3.3.0
+      - toolz==0.12.1
+      - torch==2.2.1
+      - torchdata==0.7.1
+      - triton==2.2.0
+      - typing-extensions==4.10.0
+      - urllib3==1.26.18
+      - watchdog==4.0.0
+      - websocket-client==1.5.3
+      - websockets==10.4
+      - xmltodict==0.13.0

jarvis/core/graphs.py

@@ -1,4 +1,5 @@
 """Module to generate networkx graphs."""
+
 from jarvis.core.atoms import get_supercell_dims
 from jarvis.core.specie import Specie
 from jarvis.core.utils import random_colors
@@ -11,18 +12,16 @@
 # from jarvis.core.atoms import Atoms
 from collections import defaultdict
 from typing import List, Tuple, Sequence, Optional
-
-try:
-    import torch
-    from tqdm import tqdm
-    import dgl
-except Exception as exp:
-    print("dgl/torch/tqdm is not installed.", exp)
-    pass
+import torch
+from tqdm import tqdm
+import dgl
 
 
 def canonize_edge(
-    src_id, dst_id, src_image, dst_image,
+    src_id,
+    dst_id,
+    src_image,
+    dst_image,
 ):
     """Compute canonical edge representation.
 
@@ -46,7 +45,11 @@ def canonize_edge(
 
 
 def nearest_neighbor_edges(
-    atoms=None, cutoff=8, max_neighbors=12, id=None, use_canonize=False,
+    atoms=None,
+    cutoff=8,
+    max_neighbors=12,
+    id=None,
+    use_canonize=False,
 ):
     """Construct k-NN edge list."""
     # returns List[List[Tuple[site, distance, index, image]]]
@@ -118,7 +121,8 @@ def nearest_neighbor_edges(
 
 
 def build_undirected_edgedata(
-    atoms=None, edges={},
+    atoms=None,
+    edges={},
 ):
     """Build undirected graph data from edge set.