Restructure repository around 'optimake' package (#46)

* Restructure repository around 'optimake' package

* Update CI working directory

* Update CI test invocation

.github/workflows/ci.yml

@@ -17,14 +17,10 @@ concurrency:
 
 jobs:
 
-  test-mc-optimade-package:
-    name: Test the `mc_optimade` package
+  tests:
+    name: Test the `optimake` package
     runs-on: ubuntu-latest
 
-    defaults:
-      run:
-        working-directory: src/mc_optimade
-
     steps:
     - uses: actions/checkout@v3
 
@@ -43,7 +39,7 @@ jobs:
         pip install -e .[tests,dev]
 
     - name: Run tests
-      run: pytest -vv --cov-report=xml --cov-report=term
+      run: pytest -vv --cov-report=xml --cov-report=term ./tests
 
     - name: Upload coverage
       uses: codecov/codecov-action@v3

README.md

@@ -12,7 +12,7 @@ Code for making [OPTIMADE APIs](https://optimade.org) from various formats of st
 This repository contains the following Python packages that work towards this
 aim:
 
-- `src/mc_optimade`: defines a config file format for annotating archives and registered the desired OPTIMADE entries, and a workflow for ingesting them and converting into OPTIMADE types using pre-existing parsers (e.g., ASE for structures). The archive is converted into an intermediate [OPTIMADE JSON Lines](https://github.com/Materials-Consortia/OPTIMADE/issues/471) format that can be ingested into a database and used to serve a full OPTIMADE API.
+- `src/optimake: defines a config file format for annotating archives and registered the desired OPTIMADE entries, and a workflow for ingesting them and converting into OPTIMADE types using pre-existing parsers (e.g., ASE for structures). The archive is converted into an intermediate [OPTIMADE JSON Lines](https://github.com/Materials-Consortia/OPTIMADE/issues/471) format that can be ingested into a database and used to serve a full OPTIMADE API.
 - `src/optimade_launch`: provides a platform for launching an OPTIMADE API server
 from such a JSON lines file. It does so using the
 [`optimade-python-tools`](https://github.com/Materials-Consortia/optimade-python-tools/)
@@ -33,7 +33,7 @@ entries:
 
 Run `optimake .` in the folder containing `structures.zip` and `optimade.yaml` to generate the jsonl file.
 
-See `src/mc_optimade/examples` for other supported formats and corresponding `optimade.yaml` config files.
+See `./examples` for other supported formats and corresponding `optimade.yaml` config files.
 
 
 ## Relevant links

src/mc_optimade/pyproject.toml → pyproject.toml

@@ -1,5 +1,5 @@
 [project]
-name = "mc_optimade"
+name = "optimake"
 version = "0.1"
 requires-python = ">=3.10"
 
@@ -34,8 +34,8 @@ ignore_missing_imports = true
 follow_imports = "skip"
 
 [tool.isort]
-known_first_party = "mc_optimade"
+known_first_party = "optimake"
 profile = "black"
 
 [project.scripts]
-optimake = "mc_optimade.cli:main"
+optimake = "optimake.cli:main"

src/optimake/__init__.py

@@ -0,0 +1,4 @@
+from optimake.config import Config
+from optimake.convert import convert_archive
+
+__all__ = ("Config", "convert_archive")

src/mc_optimade/mc_optimade/archive/archive_record.py → src/optimake/archive/archive_record.py

@@ -4,7 +4,7 @@
 
 import requests
 
-from mc_optimade.config import Config
+from optimake.config import Config
 
 DEFAULT_ARCHIVE_URL = "https://archive.materialscloud.org"
 

src/mc_optimade/mc_optimade/archive/cli.py → src/optimake/archive/cli.py

@@ -1,5 +1,5 @@
 import click
-from scan_records import scan_records
+from .scan_records import scan_records
 
 
 @click.group()

src/mc_optimade/mc_optimade/archive/scan_records.py → src/optimake/archive/scan_records.py

@@ -1,7 +1,7 @@
 import tqdm
 
-from mc_optimade.archive.archive_record import ArchiveRecord
-from mc_optimade.archive.utils import get_all_records, get_parsed_records
+from optimake.archive.archive_record import ArchiveRecord
+from optimake.archive.utils import get_all_records, get_parsed_records
 
 DEFAULT_ARCHIVE_URL = "https://archive.materialscloud.org/"
 

src/mc_optimade/mc_optimade/cli.py → src/optimake/cli.py

@@ -1,6 +1,6 @@
 import argparse
 from pathlib import Path
-from mc_optimade.convert import convert_archive
+from optimake.convert import convert_archive
 
 def main():
     parser = argparse.ArgumentParser(

src/mc_optimade/mc_optimade/convert.py → src/optimake/convert.py

@@ -17,7 +17,7 @@
 from .config import Config, EntryConfig, JSONLConfig, ParsedFiles, PropertyDefinition
 from .parsers import ENTRY_PARSERS, OPTIMADE_CONVERTERS, PROPERTY_PARSERS, TYPE_MAP
 
-PROVIDER_PREFIX = os.environ.get("MC_OPTIMADE_PROVIDER_PREFIX", "mcloudarchive")
+PROVIDER_PREFIX = os.environ.get("optimake_PROVIDER_PREFIX", "mcloudarchive")
 
 
 def _construct_entry_type_info(

src/mc_optimade/mc_optimade/parsers.py → src/optimake/parsers.py

@@ -10,7 +10,7 @@
 from optimade.models import EntryResource
 from pymatgen.entries.computed_entries import ComputedStructureEntry
 
-from mc_optimade.config import PropertyDefinition
+from optimake.config import PropertyDefinition
 
 
 def pybtex_to_optimade(bib_entry: Any, properties=None) -> EntryResource:

src/mc_optimade/tests/test_archive.py → tests/test_archive.py

@@ -1,14 +1,14 @@
 import traceback
 
-from mc_optimade.config import UnsupportedConfigVersion
+from optimake.config import UnsupportedConfigVersion
 
 archive_url = "https://staging-archive.materialscloud.org/"
 test_record_id = 1408
 
 
 def test_archive_record_metadata():
     """Test ArchiveRecord to read metadata."""
-    from mc_optimade.archive.archive_record import ArchiveRecord
+    from optimake.archive.archive_record import ArchiveRecord
 
     try:
         record = ArchiveRecord(test_record_id, archive_url=archive_url)
@@ -22,7 +22,7 @@ def test_archive_record_process():
     """Test ArchiveRecord to download files."""
     import os
 
-    from mc_optimade.archive.archive_record import ArchiveRecord
+    from optimake.archive.archive_record import ArchiveRecord
 
     try:
         record = ArchiveRecord(

src/mc_optimade/tests/test_convert.py → tests/test_convert.py

@@ -5,7 +5,7 @@
 import pytest
 from optimade.models import EntryInfoResource
 
-from mc_optimade.convert import convert_archive
+from optimake.convert import convert_archive
 
 EXAMPLE_ARCHIVES = (Path(__file__).parent.parent / "examples").glob("*")
 

src/mc_optimade/tests/test_yaml.py → tests/test_yaml.py

@@ -2,7 +2,7 @@
 
 import pytest
 
-from mc_optimade.config import Config
+from optimake.config import Config
 
 EXAMPLE_YAMLS = (Path(__file__).parent.parent / "examples").glob("*/optimade.yaml")