Merge pull request #22 from jacksund/jacks-edits

prep apps for initial merge
jacksund · Dec 22, 2023 · 1f6511a · 1f6511a
2 parents 5e413ad + 8a1f2aa
commit 1f6511a
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diff --git a/docs/change_log.md b/docs/change_log.md
@@ -82,23 +82,16 @@ There is one key exception to the rules above -- and that is with `MAJOR`=0 rele
 - add `django-simple-history` support to track user changes on specific models
 - add `@check_db_conn` decorator to help with database connection closures/timeouts
 - add `simmate engine start-schedules` which let's you configure periodic tasks for individual apps (e.g. check a table for updates every 5 minutes). Includes error handling and email alerts. (Note: this a quick alternative to full Prefect system)
+- add warren_lab app with Warren Lab preferred VASP settings
+- add badelf app with class oriented tools for performing BadELF analyses
+- add `simmate-badelf` command for running badelf analysis
 
 **Fixes**
 
 - fix bug where workers incorrectly grab substring tag matches (e.g. a worker submited with the tag `ex` would incorrectly grab jobs like `ex-01` or `ex-02`)
 
 --------------------------------------------------------------------------------
 
-## v0.15.0 (2023.12.21)
-
-**Enhancements**
-
-- add warren_lab app with Warren Lab preferred VASP settings
-- add badelf app with class oriented tools for performing BadELF analyses
-- add `simmate-badelf` command for running badelf analysis
-
---------------------------------------------------------------------------------
-
 ## v0.14.0 (2023.07.06)
 
 **Enhancements**

diff --git a/envs/conda/dev.yaml b/envs/conda/dev.yaml
@@ -39,6 +39,7 @@ dependencies:
     - mkdocs-material >=8.4.1, <9.2.7
     - mkdocstrings >=0.19.0, <=0.21.2
     - mkdocstrings-python >=0.7.1, <0.8.4
+    - mp-pyrho >=0.3.0, <=0.3.0
     - numpy >=1.22.0, <1.24.2
     - pandas >=2.0.0, <2.1.4
     - plotly >=5.4.0, <5.17.0

diff --git a/pyproject.toml b/pyproject.toml
@@ -31,7 +31,7 @@ name="simmate"
 # Versions should comply with PEP 440:
 # https://www.python.org/dev/peps/pep-0440/
 # https://semver.org/
-version="0.15.0"
+version="0.14.0"
 
 # Maintainer info
 authors = [{name = "Jack D. Sundberg", email = "[email protected]"}]
@@ -88,12 +88,13 @@ dependencies=[
     "toml >=0.10.2, <=0.10.2",  # for toml configuration files
     "schedule >=1.2.0, <=1.2.0",  # for running periodic tasks (prefect alternative)
     #
-    # These are from the MP stack and I want to phase them out over time
+    # These are from the MP stack and I want to phase them out over time.
+    # Some of these could be optional, but we add them for convenience.
     "pymatgen >=2022.1.9, <2023.5.32",
     "pymatgen-analysis-diffusion >=2021.4.29, <=2023.8.15",  # pymatgen-diffusion on conda
     "matminer >=0.7.6, <0.8.1",
     "ase >=3.22.1, <=3.22.1",
-    "mp-pyrho >=0.3.0",
+    "mp-pyrho >=0.3.0, <=0.3.0",  # for badelf app
 ]
 
 # optional dependencies that are not installed by default

diff --git a/src/simmate/apps/badelf/badelf_tools/chgsum.py b/src/simmate/apps/badelf/badelf_tools/chgsum.py
@@ -1,10 +1,4 @@
-#!/usr/bin/env python3
 # -*- coding: utf-8 -*-
-"""
-Created on Tue Nov 21 11:20:59 2023
-
-@author: sweav
-"""
 
 from pathlib import Path
 

diff --git a/src/simmate/apps/badelf/core/badelf.py b/src/simmate/apps/badelf/core/badelf.py
@@ -24,6 +24,7 @@
 from simmate.apps.badelf.core.partitioning import PartitioningToolkit
 from simmate.apps.badelf.core.voxel_assignment import VoxelAssignmentToolkit
 
+# BUG: we shouldn't fully turning off warnings. This should be used within a context.
 warnings.filterwarnings("ignore")
 
 

diff --git a/src/simmate/apps/badelf/core/partitioning.py b/src/simmate/apps/badelf/core/partitioning.py
@@ -1,10 +1,4 @@
-#!/usr/bin/env python3
 # -*- coding: utf-8 -*-
-"""
-Created on Sat Dec  9 16:35:48 2023
-
-@author: sweav
-"""
 
 import math
 from itertools import combinations

diff --git a/src/simmate/apps/warren_lab/README.md b/src/simmate/apps/warren_lab/README.md
diff --git a/src/simmate/apps/warren_lab/command_line/__init__.py b/src/simmate/apps/warren_lab/command_line/__init__.py
@@ -1,2 +1 @@
-#!/usr/bin/env python3
 # -*- coding: utf-8 -*-
diff --git a/src/simmate/apps/warren_lab/models/__init__.py b/src/simmate/apps/warren_lab/models/__init__.py
@@ -1,9 +1,3 @@
-#!/usr/bin/env python3
 # -*- coding: utf-8 -*-
-"""
-Created on Wed Nov 29 11:00:50 2023
-
-@author: sweav
-"""
 
 from .badelf import BadElfAnalysis
diff --git a/src/simmate/apps/warren_lab/models/badelf.py b/src/simmate/apps/warren_lab/models/badelf.py
@@ -1,10 +1,5 @@
-#!/usr/bin/env python3
 # -*- coding: utf-8 -*-
-"""
-Created on Tue Nov 21 15:18:45 2023
 
-@author: sweav
-"""
 
 from pathlib import Path
 
@@ -18,9 +13,6 @@ class BadElfAnalysis(Structure, Calculation):
     This table contains results from a BadELF analysis.
     """
 
-    class Meta:
-        app_label = "workflows"
-
     oxidation_states = table_column.JSONField(blank=True, null=True)
     """
     A list of calculated oxidation states for each site.

diff --git a/src/simmate/configuration/django/settings.py b/src/simmate/configuration/django/settings.py
@@ -251,10 +251,11 @@
     "simmate.workflows.configs.BaseWorkflowsConfig",
     "simmate.apps.configs.VaspConfig",
     "simmate.apps.configs.BaderConfig",
-    "simmate.apps.configs.BadelfConfig",
-    # "simmate.apps.configs.CleaseConfig",
     "simmate.apps.configs.EvolutionConfig",
-    "simmate.apps.configs.WarrenLabConfig",
+    # These apps may become defaults in the future:
+    # "simmate.apps.configs.BadelfConfig",
+    # "simmate.apps.configs.CleaseConfig",
+    # "simmate.apps.configs.WarrenLabConfig",
 ]
 APPLICATIONS_YAML = SIMMATE_DIRECTORY / f"{CONDA_ENV}-apps.yaml"
 # create the file if it doesn't exist yet

diff --git a/src/simmate/utilities/__init__.py b/src/simmate/utilities/__init__.py
@@ -2,7 +2,6 @@
 
 from .files import (
     archive_old_runs,
-    check_required_files,
     chunk_read,
     copy_directory,
     copy_files_from_directory,

diff --git a/src/simmate/utilities/files.py b/src/simmate/utilities/files.py
@@ -57,19 +57,6 @@ def get_directory(directory: Path | str = None) -> Path:
     return directory_cleaned.absolute()
 
 
-def check_required_files(directory: Path, required_files: list):
-    """
-    Checks to make sure that all the files in a folder exist. Otherwise raises
-    an error.
-    """
-    if not all((directory / file).exists() for file in required_files):
-        raise Exception(
-            f"""Make sure your `setup` method directory source is defined correctly. 
-        The following files must exist in the directory where 
-        this task is ran but some are missing: {required_files}"""
-        )
-
-
 def copy_files_from_directory(
     files_to_copy: list[Path],
     directory_old: Path,

diff --git a/src/simmate/website/workflows/migrations/0001_initial.py b/src/simmate/website/workflows/migrations/0001_initial.py
@@ -1,4 +1,4 @@
-# Generated by Django 4.1.5 on 2023-12-20 20:31
+# Generated by Django 4.2.6 on 2023-11-19 21:07
 
 import django.db.models.deletion
 from django.db import migrations, models

diff --git a/src/simmate/website/workflows/migrations/0002_badelfanalysis.py b/src/simmate/website/workflows/migrations/0002_badelfanalysis.py
diff --git a/src/simmate/workflows/test/test_workflows_utilities.py b/src/simmate/workflows/test/test_workflows_utilities.py
@@ -35,9 +35,9 @@ def test_get_workflow_types():
 def test_list_of_all_workflows():
     assert get_all_workflow_names() == [
         # "cluster-expansion.clease.bulk-structure",
-        "bad-elf-analysis.badelf.badelf",
-        "bad-elf-analysis.badelf.badelf-hse",
-        "bad-elf-analysis.badelf.badelf-pbesol",
+        # "bad-elf-analysis.badelf.badelf",
+        # "bad-elf-analysis.badelf.badelf-hse",
+        # "bad-elf-analysis.badelf.badelf-pbesol",
         "customized.toolkit.user-config",
         "diffusion.vasp.neb-all-paths-mit",
         "diffusion.vasp.neb-all-paths-warren-lab",
@@ -55,9 +55,9 @@ def test_list_of_all_workflows():
         "electronic-structure.vasp.matproj-density-of-states-hse",
         "electronic-structure.vasp.matproj-full",
         "electronic-structure.vasp.matproj-hse-full",
-        "nested.vasp.warren-lab-relaxation-static-hse-hse",
-        "nested.vasp.warren-lab-relaxation-static-pbe-hse",
-        "nested.vasp.warren-lab-relaxation-static-pbe-pbe",
+        # "nested.vasp.warren-lab-relaxation-static-hse-hse",
+        # "nested.vasp.warren-lab-relaxation-static-pbe-hse",
+        # "nested.vasp.warren-lab-relaxation-static-pbe-pbe",
         "population-analysis.bader.badelf",
         "population-analysis.bader.bader",
         "population-analysis.bader.combine-chgcars",
@@ -82,14 +82,14 @@ def test_list_of_all_workflows():
         "relaxation.vasp.quality03",
         "relaxation.vasp.quality04",
         "relaxation.vasp.staged",
-        "relaxation.vasp.warren-lab-hse",
-        "relaxation.vasp.warren-lab-hse-with-wavecar",
-        "relaxation.vasp.warren-lab-hsesol",
-        "relaxation.vasp.warren-lab-pbe",
-        "relaxation.vasp.warren-lab-pbe-metal",
-        "relaxation.vasp.warren-lab-pbe-with-wavecar",
-        "relaxation.vasp.warren-lab-pbesol",
-        "relaxation.vasp.warren-lab-scan",
+        # "relaxation.vasp.warren-lab-hse",
+        # "relaxation.vasp.warren-lab-hse-with-wavecar",
+        # "relaxation.vasp.warren-lab-hsesol",
+        # "relaxation.vasp.warren-lab-pbe",
+        # "relaxation.vasp.warren-lab-pbe-metal",
+        # "relaxation.vasp.warren-lab-pbe-with-wavecar",
+        # "relaxation.vasp.warren-lab-pbesol",
+        # "relaxation.vasp.warren-lab-scan",
         # "relaxation.vasp.staged-cluster",
         "restart.toolkit.automatic",
         # "static-energy.vasp.cluster-high-qe",
@@ -103,14 +103,14 @@ def test_list_of_all_workflows():
         "static-energy.vasp.prebadelf-matproj",
         "static-energy.vasp.prebader-matproj",
         "static-energy.vasp.quality04",
-        "static-energy.vasp.warren-lab-hse",
-        "static-energy.vasp.warren-lab-hsesol",
-        "static-energy.vasp.warren-lab-pbe",
-        "static-energy.vasp.warren-lab-pbe-metal",
-        "static-energy.vasp.warren-lab-pbesol",
-        "static-energy.vasp.warren-lab-prebadelf-hse",
-        "static-energy.vasp.warren-lab-prebadelf-pbesol",
-        "static-energy.vasp.warren-lab-scan",
+        # "static-energy.vasp.warren-lab-hse",
+        # "static-energy.vasp.warren-lab-hsesol",
+        # "static-energy.vasp.warren-lab-pbe",
+        # "static-energy.vasp.warren-lab-pbe-metal",
+        # "static-energy.vasp.warren-lab-pbesol",
+        # "static-energy.vasp.warren-lab-prebadelf-hse",
+        # "static-energy.vasp.warren-lab-prebadelf-pbesol",
+        # "static-energy.vasp.warren-lab-scan",
         "structure-prediction.toolkit.chemical-system",
         "structure-prediction.toolkit.fixed-composition",
         "structure-prediction.toolkit.new-individual",
@@ -196,28 +196,28 @@ def test_get_custom_workflow(tmp_path):
 
 def test_get_unique_paramters():
     assert get_unique_parameters() == [
-        "algorithm",
+        # "algorithm",
         "angle_tolerance",
         "best_survival_cutoff",
-        "check_for_covalency",
+        # "check_for_covalency",
         "chemical_system",
         # "cluster_diameter",
         "command",
         "composition",
         "compress_output",
         "convergence_cutoff",
-        "cores",
+        # "cores",
         # "convergence_limit",
         # "current_generation",
         "diffusion_analysis_id",
         "directory",
         "directory_new",
         "directory_old",
-        "electride_connection_cutoff",
-        "electride_finder_cutoff",
+        # "electride_connection_cutoff",
+        # "electride_finder_cutoff",
         "empty_ion",
         "empty_sites",
-        "find_electrides",
+        # "find_electrides",
         "fitness_field",
         # "formula_unit",
         "input_parameters",