Remove circular dependence from MP software stack (#532)

* remove circular software dependence (robocrys depends on mp_api, mp_api on emmet-core, emmet-core on robocrys through extras) added by switching from pymatgen to mp_api

* organize tests / test data outside package / change formula_db.json.gz format to save disk space

* update / run precommit

* disable progress bar in matminer json loading

Author: esoteric-ephemera

.github/workflows/tests.yml

@@ -18,10 +18,10 @@ jobs:
         run: |
           conda install --quiet --yes -c conda-forge openbabel pip ruamel.yaml
           pip install -r requirements.txt
-          pip install -e .[tests]
+          pip install -e .[tests,cli]
 
       - name: Test
-        run: pytest --cov=robocrys --cov-report=xml --cov-config=.coveragerc
+        run: pytest --cov=robocrys --cov-report=xml --cov-config=.coveragerc tests/
 
   docs:
     runs-on: ubuntu-latest
@@ -37,7 +37,7 @@ jobs:
         run: |
           python -m pip install --upgrade pip
           pip install -r requirements.txt
-          pip install -e .[docs]
+          pip install -e .[docs,cli]
 
       - name: Build
         run: sphinx-build docs/src docs_build

.pre-commit-config.yaml

@@ -1,28 +1,49 @@
+exclude: ^(docs|tests|dev_scripts|.github)
+
+default_language_version:
+  python: python3.11
+
+ci:
+  autoupdate_schedule: yearly
+  skip: [flake8, autoflake, mypy]
+
 repos:
-  - repo: https://github.com/myint/autoflake
-    rev: v1.4
+
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.4.3
     hooks:
-    - id: autoflake
-      args: [--in-place, --remove-all-unused-imports, --remove-unused-variable, --ignore-init-module-imports]
+      - id: ruff
+        args: [--fix, --unsafe-fixes]
+
   - repo: https://github.com/psf/black
-    rev: 21.4b2
+    rev: 24.2.0
     hooks:
-    - id: black
-  - repo: https://gitlab.com/pycqa/flake8
-    rev: 3.9.1
-    hooks:
-      - id: flake8
-        args: [--max-line-length=125, "--extend-ignore=E203,W503"]
-        language_version: python3
+      - id: black
+
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v3.4.0
+    rev: v4.5.0
     hooks:
       - id: check-yaml
       - id: end-of-file-fixer
       - id: trailing-whitespace
-  - repo: https://github.com/pycqa/isort
-    rev: 5.8.0
+
+  - repo: https://github.com/PyCQA/autoflake
+    rev: v2.3.0
+    hooks:
+      - id: autoflake
+        args:
+          - --in-place
+          - --remove-unused-variables
+          - --remove-all-unused-imports
+          - --expand-star-imports
+          - --ignore-init-module-imports
+
+  - repo: https://github.com/pre-commit/mirrors-mypy
+    rev: v1.8.0
     hooks:
-      - id: isort
-        name: isort (python)
-        args: [--profile=black]
+      - id: mypy
+        files: ^pymatgen/
+        args:
+          - --namespace-packages
+          - --explicit-package-bases
+        additional_dependencies: ['types-requests']

requirements.txt

@@ -8,5 +8,3 @@ matminer==0.9.2
 monty==2024.7.30
 pubchempy==1.0.4
 pybtex==0.24.0
-mp-api==0.42.2
-boto3

robocrys/__init__.py

@@ -2,6 +2,7 @@
 
 isort:skip_file
 """
+
 from __future__ import annotations
 
 from robocrys._version import __version__

robocrys/adapter.py

@@ -1,6 +1,7 @@
 """This module implements a class to resolve the symbolic references in condensed
 structure data.
 """
+
 from __future__ import annotations
 
 from typing import Any

robocrys/cli.py

@@ -1,12 +1,17 @@
 """This module contains a script for using robocrys from the command line."""
+
 from __future__ import annotations
 
 import argparse
 import sys
 import warnings
 
 from pymatgen.core.structure import Structure
-from mp_api.client import MPRestError
+
+try:
+    from mp_api.client import MPRestError
+except ImportError:
+    MPRestError = None
 
 from robocrys import StructureCondenser, StructureDescriber, __version__
 
@@ -210,6 +215,13 @@ def main():
 
     except FileNotFoundError:
         if args.filename[:3] in ["mp-", "mvc"]:
+
+            if MPRestError is None:
+                raise ImportError(
+                    "Please install the Materials Project API using"
+                    "`pip install mp_api`"
+                )
+
             from mp_api.client import MPRester
 
             mpr = MPRester(args.api_key)

robocrys/condense/component.py

@@ -1,4 +1,5 @@
 """This module implements functions for handling structure components."""
+
 from __future__ import annotations
 
 from copy import deepcopy

robocrys/condense/condenser.py

@@ -1,4 +1,5 @@
 """This module defines a class for condensing structures into dict representations."""
+
 from __future__ import annotations
 
 from typing import TYPE_CHECKING, Any

robocrys/condense/formula_db.json.gz

@@ -62,7 +62,7 @@ def __init__(
     ):
         self.mineral_db = mineral_db if mineral_db is not None else _mineral_db_file
         if isinstance(self.mineral_db, (str, Path)):
-            self.mineral_db = load_dataframe_from_json(self.mineral_db)
+            self.mineral_db = load_dataframe_from_json(self.mineral_db, pbar=False)
 
         self.initial_ltol = initial_ltol
         self.initial_stol = initial_stol