Merge branch 'JaGeo:main' into structure_graphs

.github/workflows/python-package.yml

@@ -17,7 +17,7 @@ jobs:
       fail-fast: false
       matrix:
         python-version: ["3.8", "3.9", "3.10", "3.11"]
-        split: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10]  # Number of splits
+        split: [1, 2, 3, 4, 5]  # Number of splits
 
     steps:
     - uses: actions/checkout@v3
@@ -39,8 +39,10 @@ jobs:
         # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
         flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
     - name: Test with pytest and coverage
+      # run this locally to update tests durations
+      # pytest --cov=lobsterpy --cov-append --splits 1 --group 1 --durations-path ./lobsterpy/TestData/.pytest-split-durations --store-durations
       run: |
-        pytest --cov=lobsterpy --cov-append --splits 10 --group ${{ matrix.split }} --durations-path ./lobsterpy/.pytest-split-durations
+        pytest --cov=lobsterpy --cov-append --splits 5 --group ${{ matrix.split }} --durations-path ./lobsterpy/TestData/.pytest-split-durations
     - name: Upload coverage
       uses: actions/upload-artifact@v3
       with:

CHANGELOG.md

@@ -1,3 +1,5 @@
+## v0.3.0
+- addition of an interactive plotter by @naik-aakash and @kaueltzen. Reviews by @ajjackson and @jageo
 ## v0.2.9
 - fix the error handling in cases ChemEnv cannot determine a coordination environment and we use coordination numbers instead for the cation-anion mode
 

docs/source/commandlineinterface.rst

@@ -227,6 +227,20 @@ command. Below is an example and sample output using this command.
    
 .. image:: Lobsterpy_tutorial_files/ICOHP.png
 
+-  ``lobsterpy automatic-plot-ia`` command can be used to obtain a interactive plot of analysis automatically. It will evaluate all COHPs with ICOHP values down to
+   10% of the strongest ICOHP. You can enforce an analysis of all bonds
+   by using ``lobsterpy automatic-plot-ia --allbonds``. Currently, the
+   computed Mulliken charges will be used to determine cations and
+   anions. If no CHARGE.lobster is available, the algorithm will fall
+   back to the BondValence analysis from pymatgen. Please be aware that
+   LobsterPy can only analyze bonds that have been included in the
+   initial Lobster computation. Below is an example and sample output
+   using this command. You can also obtain label resolved plot using
+   ``lobsterpy automatic-plot-ia --allbonds --label-resolved`` option
+
+.. raw:: html
+   :file: Lobsterpy_tutorial_files/CdF2.html
+
 2. Plotting of COHPs/COBIs/COOPs
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 

docs/source/conf.py

@@ -48,7 +48,7 @@
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
 # This pattern also affects html_static_path and html_extra_path.
-exclude_patterns = ["../../lobsterpy/test","../../lobsterpy/cohp/test","../../lobsterpy/TestData","Thumbs.db", ".DS_Store",]
+exclude_patterns = ["../../lobsterpy/test","../../lobsterpy/cohp/test","../../lobsterpy/plotting/test","../../lobsterpy/TestData","Thumbs.db", ".DS_Store",]
 
 def run_apidoc(_):
     import subprocess
@@ -57,9 +57,10 @@ def run_apidoc(_):
     output_path = os.path.abspath(os.path.dirname(__file__))
     excludes = glob.glob(os.path.join(output_path, "../../lobsterpy/cohp/test"))
     excludes1 = glob.glob(os.path.join(output_path, "../../lobsterpy/test"))
+    excludes2 = glob.glob(os.path.join(output_path, "../../lobsterpy/plotting/test"))
     module = os.path.join(output_path, "../../lobsterpy")
     cmd_path = "sphinx-apidoc"
-    command = [cmd_path, "-e", "-o", output_path, module, " ".join(excludes)," ".join(excludes1), "--force"]
+    command = [cmd_path, "-e", "-o", output_path, module, " ".join(excludes)," ".join(excludes1)," ".join(excludes2), "--force"]
     subprocess.check_call(command)
 
 

docs/source/pythoninterface.rst

@@ -41,9 +41,15 @@ Import the necessary modules
     # Automatic plots
     describe.plot_cohps(ylim=[-10, 2], xlim=[-4, 4])
 
+.. image:: Lobsterpy_tutorial_files/Lobsterpy_tutorial_38_0.png
+
+.. code:: ipython3
 
+    # Automatic interactive plots
+    describe.plot_interactive_cohps()
 
-.. image:: Lobsterpy_tutorial_files/Lobsterpy_tutorial_38_0.png
+.. raw:: html
+   :file: Lobsterpy_tutorial_files/CdF2.html
 
 
 .. code:: ipython3

lobsterpy/TestData/.pytest-split-durations

@@ -0,0 +1,62 @@
+{
+    "lobsterpy/cohp/test/test_analyze.py::TestAnalyse::test_ICOHP_sum_CdF": 74.60168297588825,
+    "lobsterpy/cohp/test/test_analyze.py::TestAnalyse::test_ICOHP_sum_NaCl": 70.55211293883622,
+    "lobsterpy/cohp/test/test_analyze.py::TestAnalyse::test_all_attributes_BaTiO3": 71.29058763198555,
+    "lobsterpy/cohp/test/test_analyze.py::TestAnalyse::test_all_attributes_CdF": 72.19752324093133,
+    "lobsterpy/cohp/test/test_analyze.py::TestAnalyse::test_all_attributes_K3Sb": 72.58499348722398,
+    "lobsterpy/cohp/test/test_analyze.py::TestAnalyse::test_all_attributes_K3Sb_all": 72.2198564982973,
+    "lobsterpy/cohp/test/test_analyze.py::TestAnalyse::test_all_attributes_NaCl_Mulliken": 70.49185390630737,
+    "lobsterpy/cohp/test/test_analyze.py::TestAnalyse::test_all_attributes_NaCl_all": 66.83933831006289,
+    "lobsterpy/cohp/test/test_analyze.py::TestAnalyse::test_all_attributes_NaCl_nan": 64.23106821579859,
+    "lobsterpy/cohp/test/test_analyze.py::TestAnalyse::test_all_attributes_NaCl_valences": 66.02353994967416,
+    "lobsterpy/cohp/test/test_analyze.py::TestAnalyse::test_all_attributes_NaSbF6": 67.69128251960501,
+    "lobsterpy/cohp/test/test_analyze.py::TestAnalyse::test_all_attributes_NaSbF6_anbd": 77.39906527288258,
+    "lobsterpy/cohp/test/test_analyze.py::TestAnalyse::test_exception": 74.9940577801317,
+    "lobsterpy/cohp/test/test_analyze.py::TestAnalyse::test_final_dicts": 71.91315609263256,
+    "lobsterpy/cohp/test/test_describe.py::TestDescribe::test_coordination_environment_to_text": 60.532792599871755,
+    "lobsterpy/cohp/test/test_describe.py::TestDescribe::test_plot": 88.35905195400119,
+    "lobsterpy/cohp/test/test_describe.py::TestDescribe::test_text": 58.00953777041286,
+    "lobsterpy/cohp/test/test_describe.py::TestDescribe::test_write_description": 62.47553640883416,
+    "lobsterpy/plotting/test/test_plotting.py::InteractiveCohpPlotterTest::test_add_all_relevant_cohps_K3Sb": 48.36465826490894,
+    "lobsterpy/plotting/test/test_plotting.py::InteractiveCohpPlotterTest::test_add_all_relevant_cohps_NaCl": 14.395964342169464,
+    "lobsterpy/plotting/test/test_plotting.py::InteractiveCohpPlotterTest::test_add_cohps_by_lobster_label_NaCl": 14.143686045892537,
+    "lobsterpy/plotting/test/test_plotting.py::InteractiveCohpPlotterTest::test_add_cohps_from_plot_data": 14.694280326366425,
+    "lobsterpy/plotting/test/test_plotting.py::InteractiveCohpPlotterTest::test_add_cohps_from_plot_data_json": 18.901866920292377,
+    "lobsterpy/plotting/test/test_plotting.py::InteractiveCohpPlotterTest::test_plot_colors": 50.03976339753717,
+    "lobsterpy/plotting/test/test_plotting.py::InteractiveCohpPlotterTest::test_plot_labels": 14.167344754561782,
+    "lobsterpy/plotting/test/test_plotting.py::TestPlotterExceptions::test_plotter_exception": 0.0038974578492343426,
+    "lobsterpy/test/test_cli.py::TestCLI::test_cli_errors[args0-IndexError]": 0.19080257462337613,
+    "lobsterpy/test/test_cli.py::TestCLI::test_cli_errors[args1-IndexError]": 0.20083071431145072,
+    "lobsterpy/test/test_cli.py::TestCLI::test_cli_errors[args2-IndexError]": 0.22901855362579226,
+    "lobsterpy/test/test_cli.py::TestCLI::test_cli_interactive_plotter": 0.9448978300206363,
+    "lobsterpy/test/test_cli.py::TestCLI::test_cli_results[args0]": 1.3463104199618101,
+    "lobsterpy/test/test_cli.py::TestCLI::test_cli_results[args10]": 0.37567619839683175,
+    "lobsterpy/test/test_cli.py::TestCLI::test_cli_results[args11]": 0.49541555624455214,
+    "lobsterpy/test/test_cli.py::TestCLI::test_cli_results[args12]": 0.3643593993037939,
+    "lobsterpy/test/test_cli.py::TestCLI::test_cli_results[args13]": 0.3989682081155479,
+    "lobsterpy/test/test_cli.py::TestCLI::test_cli_results[args14]": 0.3308272184804082,
+    "lobsterpy/test/test_cli.py::TestCLI::test_cli_results[args15]": 0.6352701694704592,
+    "lobsterpy/test/test_cli.py::TestCLI::test_cli_results[args16]": 1.414562267716974,
+    "lobsterpy/test/test_cli.py::TestCLI::test_cli_results[args17]": 0.6187749514356256,
+    "lobsterpy/test/test_cli.py::TestCLI::test_cli_results[args18]": 0.45203554816544056,
+    "lobsterpy/test/test_cli.py::TestCLI::test_cli_results[args1]": 1.277391605079174,
+    "lobsterpy/test/test_cli.py::TestCLI::test_cli_results[args2]": 1.110627113841474,
+    "lobsterpy/test/test_cli.py::TestCLI::test_cli_results[args3]": 0.8713983865454793,
+    "lobsterpy/test/test_cli.py::TestCLI::test_cli_results[args4]": 0.7319109700620174,
+    "lobsterpy/test/test_cli.py::TestCLI::test_cli_results[args5]": 0.9687392474152148,
+    "lobsterpy/test/test_cli.py::TestCLI::test_cli_results[args6]": 0.9414747003465891,
+    "lobsterpy/test/test_cli.py::TestCLI::test_cli_results[args7]": 0.48369616316631436,
+    "lobsterpy/test/test_cli.py::TestCLI::test_cli_results[args8]": 0.5601856517605484,
+    "lobsterpy/test/test_cli.py::TestCLI::test_cli_results[args9]": 0.37080864515155554,
+    "lobsterpy/test/test_cli.py::TestCLI::test_generate_ref_data": 0.004219974856823683,
+    "lobsterpy/test/test_cli.py::TestCLI::test_gz_cli_plot": 3.995695054065436,
+    "lobsterpy/test/test_cli.py::TestCLI::test_gz_file_cli": 14.55165875563398,
+    "lobsterpy/test/test_cli.py::TestCLI::test_gz_file_cli_lobsterinput_generation": 0.01727287331596017,
+    "lobsterpy/test/test_cli.py::TestCLI::test_hideplot_cli": 3.988109601661563,
+    "lobsterpy/test/test_cli.py::TestCLI::test_iaplot_saved": 0.8917648741044104,
+    "lobsterpy/test/test_cli.py::TestCLI::test_json_saved": 1.117712059058249,
+    "lobsterpy/test/test_cli.py::TestCLI::test_lobsterin_generation": 0.979003781452775,
+    "lobsterpy/test/test_cli.py::TestCLI::test_lobsterin_generation_error": 0.9563554651103914,
+    "lobsterpy/test/test_cli.py::TestCLI::test_lobsterin_generation_error_userbasis": 0.01105657871812582,
+    "lobsterpy/test/test_cli.py::TestCLI::test_plot_saved": 0.9114251169376075
+}

lobsterpy/cli.py

@@ -16,7 +16,7 @@
 
 from lobsterpy.cohp.analyze import Analysis
 from lobsterpy.cohp.describe import Description
-from lobsterpy.plotting import PlainCohpPlotter, get_style_list
+from lobsterpy.plotting import PlainCohpPlotter, get_style_list, InteractiveCohpPlotter
 
 
 def main() -> None:
@@ -199,6 +199,14 @@ def get_parser() -> argparse.ArgumentParser:
     plotting_group.add_argument(
         "--fontsize", "--font-size", type=float, default=None, help="Base font size"
     )
+    plotting_group.add_argument(
+        "--labelresolved",
+        "--label-resolved",
+        action="store_true",
+        help="Will create automatic interactive plots with all relevant bond labels. "
+        "If not set, plots will consists of summed cohps. (This argument works only"
+        "for interactive plots) ",
+    )
 
     auto_parent = argparse.ArgumentParser(add_help=False)
     auto_group = auto_parent.add_argument_group("Automatic analysis")
@@ -244,6 +252,16 @@ def get_parser() -> argparse.ArgumentParser:
         ),
     )
 
+    subparsers.add_parser(
+        "automatic-plot-ia",
+        aliases=["automaticplotia", "autoplotia", "auto-plot-ia"],
+        parents=[input_parent, auto_parent, plotting_parent],
+        help=(
+            "Creates an interactive plot of most important COHPs automatically. Implementation "
+            "of COBIs and COOPs will follow."
+        ),
+    )
+
     subparsers.add_parser(
         "create-inputs",
         aliases=["createinputs"],
@@ -349,6 +367,11 @@ def run(args):
         "description",
         "automatic-plot",
         "plot",
+        "automatic-plot-ia",
+        "interactplot",
+        "automaticplotia",
+        "auto-plot-ia",
+        "autoplotia",
     ]:
         # Check for .gz files exist for default values and update accordingly
         default_files = {
@@ -373,7 +396,17 @@ def run(args):
     if args.action in ["automaticplot", "autoplot", "auto-plot"]:
         args.action = "automatic-plot"
 
-    if args.action in ["description", "automatic-plot"]:
+    if args.action in ["automaticplotia", "automatic-plot-ia", "auto-plot-ia"]:
+        args.action = "automaticplotia"
+
+    if args.action in [
+        "description",
+        "automatic-plot",
+        "automatic-plot-ia",
+        "automaticplotia",
+        "auto-plot-ia",
+        "autoplotia",
+    ]:
         if args.allbonds:
             whichbonds = "all"
         else:
@@ -395,7 +428,14 @@ def run(args):
             with open(args.json, "w") as fd:
                 json.dump(analysedict, fd)
 
-    if args.action in ["plot", "automatic-plot"]:
+    if args.action in [
+        "plot",
+        "automatic-plot",
+        "automaticplotia",
+        "automatic-plot-ia",
+        "auto-plot-ia",
+        "autoplotia",
+    ]:
         style_kwargs = {}
         style_kwargs.update(_user_figsize(args.width, args.height))
         if args.fontsize:
@@ -422,7 +462,25 @@ def run(args):
             filename=args.save_plot,
             title=args.title,
             sigma=sigma,
-            skip_show=args.hideplot,
+            hide=args.hideplot,
+        )
+
+    if args.action in [
+        "automatic-plot-ia",
+        "automaticplotia",
+        "auto-plot-ia",
+        "autoplotia",
+    ]:
+        describe.plot_interactive_cohps(
+            ylim=args.ylim,
+            xlim=args.xlim,
+            integrated=args.integrated,
+            save_as_html=args.save_plot,
+            filename=args.save_plot,
+            title=args.title,
+            sigma=sigma,
+            hide=args.hideplot,
+            label_resolved=args.labelresolved,
         )
 
     if args.action == "plot":