From a19ba655e7201da342eaeb64628b17620ac01bea Mon Sep 17 00:00:00 2001
From: Kristjan Eimre <eimrek@users.noreply.github.com>
Date: Tue, 30 Jul 2024 19:38:49 +0300
Subject: [PATCH] rename python package to optimade-maker (#63)

---
 .github/workflows/ci.yml                      | 63 +++++++++----------
 README.md                                     | 14 ++---
 pyproject.toml                                |  6 +-
 src/optimade_maker/__init__.py                |  4 ++
 .../archive/__init__.py                       |  0
 .../archive/archive_record.py                 |  2 +-
 .../archive/cli.py                            |  0
 .../archive/scan_records.py                   |  4 +-
 .../archive/utils.py                          |  0
 src/{optimake => optimade_maker}/cli.py       |  6 +-
 src/{optimake => optimade_maker}/config.py    |  0
 src/{optimake => optimade_maker}/convert.py   |  0
 src/{optimake => optimade_maker}/logger.py    |  0
 src/{optimake => optimade_maker}/parsers.py   |  2 +-
 src/{optimake => optimade_maker}/serve.py     |  4 +-
 src/optimake/__init__.py                      |  4 --
 tests/test_archive.py                         |  6 +-
 tests/test_convert.py                         |  4 +-
 tests/test_yaml.py                            |  2 +-
 19 files changed, 60 insertions(+), 61 deletions(-)
 create mode 100644 src/optimade_maker/__init__.py
 rename src/{optimake => optimade_maker}/archive/__init__.py (100%)
 rename src/{optimake => optimade_maker}/archive/archive_record.py (99%)
 rename src/{optimake => optimade_maker}/archive/cli.py (100%)
 rename src/{optimake => optimade_maker}/archive/scan_records.py (90%)
 rename src/{optimake => optimade_maker}/archive/utils.py (100%)
 rename src/{optimake => optimade_maker}/cli.py (93%)
 rename src/{optimake => optimade_maker}/config.py (100%)
 rename src/{optimake => optimade_maker}/convert.py (100%)
 rename src/{optimake => optimade_maker}/logger.py (100%)
 rename src/{optimake => optimade_maker}/parsers.py (98%)
 rename src/{optimake => optimade_maker}/serve.py (97%)
 delete mode 100644 src/optimake/__init__.py

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index ea9718e..e2a8d0d 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -4,7 +4,7 @@ on:
   pull_request:
   push:
     branches:
-    - main
+      - main
 
 env:
   PYTEST_ADDOPTS: "--color=yes"
@@ -16,38 +16,37 @@ concurrency:
   cancel-in-progress: true
 
 jobs:
-
   tests:
-    name: Test the `optimake` package
+    name: Test the `optimade-maker` package
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v3
-
-    - name: Set up Python 3.10
-      uses: actions/setup-python@v4
-      with:
-        python-version: '3.10'
-        cache: 'pip'
-        cache-dependency-path: |
-          pyproject.toml
-
-    - name: Install latest compatible versions of immediate dependencies
-      run: |
-        python -m pip install --upgrade pip
-        pip install -U setuptools wheel
-        pip install -e .[tests,dev]
-
-    - name: Run linters
-      run: |
-        pre-commit run --all-files
-
-    - name: Run tests
-      run: pytest -vv --cov-report=xml --cov-report=term ./tests
-
-    - name: Upload coverage
-      uses: codecov/codecov-action@v3
-      with:
-        name: project
-        file: ./coverage.xml
-        flags: project
+      - uses: actions/checkout@v3
+
+      - name: Set up Python 3.10
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.10"
+          cache: "pip"
+          cache-dependency-path: |
+            pyproject.toml
+
+      - name: Install latest compatible versions of immediate dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install -U setuptools wheel
+          pip install -e .[tests,dev]
+
+      - name: Run linters
+        run: |
+          pre-commit run --all-files
+
+      - name: Run tests
+        run: pytest -vv --cov-report=xml --cov-report=term ./tests
+
+      - name: Upload coverage
+        uses: codecov/codecov-action@v3
+        with:
+          name: project
+          file: ./coverage.xml
+          flags: project
diff --git a/README.md b/README.md
index 0f42b3c..9666e9c 100644
--- a/README.md
+++ b/README.md
@@ -6,11 +6,11 @@
 
 # <div align="center">optimade-maker</div>
 
-[![PyPI - Version](https://img.shields.io/pypi/v/optimake?color=4CC61E)](https://pypi.org/project/optimake/)
+[![PyPI - Version](https://img.shields.io/pypi/v/optimade-maker?color=4CC61E)](https://pypi.org/project/optimade-maker/)
 
 Tools for making [OPTIMADE APIs](https://optimade.org) from various formats of structural data (e.g. an archive of CIF files).
 
-This repository contains the `src/optimake` Python packages that work towards this aim. Features include
+This repository contains the `src/optimade-maker` Python package and the corresponding CLI tool `optimake` that work towards this aim. Features include
 
 - definition of a config file format (`optimade.yaml`) for annotating data archives to be used in the OPTIMADE ecosystem;
 - conversion of the raw data into corresponding OPTIMADE types using pre-existing parsers (e.g., ASE for structures);
@@ -24,7 +24,7 @@ See `./examples` for a more complete set of supported formats and corresponding
 
 ### Annotating with `optimade.yaml`
 
-To annotate your structural data for `optimake`, the data archive needs to be accompanied by an `optimade.yaml` config file. The following is a simple example for a zip archive (`structures.zip`) of cif files together with an optional property file (`data.csv`):
+To annotate your structural data for `optimade-maker`, the data archive needs to be accompanied by an `optimade.yaml` config file. The following is a simple example for a zip archive (`structures.zip`) of cif files together with an optional property file (`data.csv`):
 
 ```yaml
 config_version: 0.1.0
@@ -49,7 +49,7 @@ entries:
 
 ### Structure `id`s and property files
 
-`optimake` will assign an `id` for each structure based on its full path in the archive, following a simple deterministic rule: from the set of all archive paths, the maximum common path prefix and postfix (including file extensions) are removed. E.g.
+`optimade-maker` will assign an `id` for each structure based on its full path in the archive, following a simple deterministic rule: from the set of all archive paths, the maximum common path prefix and postfix (including file extensions) are removed. E.g.
 
 ```
 structures.zip/cifs/set1/101.cif
@@ -71,7 +71,7 @@ structures.zip/cifs/set2/102.cif,3.2
 Install with
 
 ```bash
-pip install .
+pip install optimade-maker
 ```
 
 this will also make the `optimake` CLI utility available.
@@ -83,9 +83,9 @@ For a folder containing the data archive and the `optimade.yaml` file (such as i
 
 For more detailed information see also `optimake --help`.
 
-## `optimake` JSONLines Format
+## `optimade-maker` JSONLines Format
 
-As described above, `optimake` works via an intermediate JSONLines file representation of an OPTIMADE API (see also the [corresponding issue in the specification](https://github.com/Materials-Consortia/OPTIMADE/issues/471)).
+As described above, `optimade-maker` works via an intermediate JSONLines file representation of an OPTIMADE API (see also the [corresponding issue in the specification](https://github.com/Materials-Consortia/OPTIMADE/issues/471)).
 This file should provide enough metadata to spin up an OPTIMADE API with many different entry types.
 The format is as follows:
 
diff --git a/pyproject.toml b/pyproject.toml
index af28ba7..24f5351 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,5 +1,5 @@
 [project]
-name = "optimake"
+name = "optimade-maker"
 description = "Tools for making OPTIMADE APIs from raw structural data."
 readme = "README.md"
 version = "0.2.2"
@@ -51,8 +51,8 @@ ignore_missing_imports = true
 follow_imports = "skip"
 
 [tool.isort]
-known_first_party = "optimake"
+known_first_party = "optimade_maker"
 profile = "black"
 
 [project.scripts]
-optimake = "optimake.cli:cli"
+optimake = "optimade_maker.cli:cli"
diff --git a/src/optimade_maker/__init__.py b/src/optimade_maker/__init__.py
new file mode 100644
index 0000000..3e6689d
--- /dev/null
+++ b/src/optimade_maker/__init__.py
@@ -0,0 +1,4 @@
+from optimade_maker.config import Config
+from optimade_maker.convert import convert_archive
+
+__all__ = ("Config", "convert_archive")
diff --git a/src/optimake/archive/__init__.py b/src/optimade_maker/archive/__init__.py
similarity index 100%
rename from src/optimake/archive/__init__.py
rename to src/optimade_maker/archive/__init__.py
diff --git a/src/optimake/archive/archive_record.py b/src/optimade_maker/archive/archive_record.py
similarity index 99%
rename from src/optimake/archive/archive_record.py
rename to src/optimade_maker/archive/archive_record.py
index 5decbbf..1da36c4 100644
--- a/src/optimake/archive/archive_record.py
+++ b/src/optimade_maker/archive/archive_record.py
@@ -4,7 +4,7 @@
 
 import requests
 
-from optimake.config import Config
+from optimade_maker.config import Config
 
 DEFAULT_ARCHIVE_URL = "https://archive.materialscloud.org"
 
diff --git a/src/optimake/archive/cli.py b/src/optimade_maker/archive/cli.py
similarity index 100%
rename from src/optimake/archive/cli.py
rename to src/optimade_maker/archive/cli.py
diff --git a/src/optimake/archive/scan_records.py b/src/optimade_maker/archive/scan_records.py
similarity index 90%
rename from src/optimake/archive/scan_records.py
rename to src/optimade_maker/archive/scan_records.py
index cc92908..374db00 100644
--- a/src/optimake/archive/scan_records.py
+++ b/src/optimade_maker/archive/scan_records.py
@@ -1,7 +1,7 @@
 import tqdm
 
-from optimake.archive.archive_record import ArchiveRecord
-from optimake.archive.utils import get_all_records, get_parsed_records
+from optimade_maker.archive.archive_record import ArchiveRecord
+from optimade_maker.archive.utils import get_all_records, get_parsed_records
 
 DEFAULT_ARCHIVE_URL = "https://archive.materialscloud.org/"
 
diff --git a/src/optimake/archive/utils.py b/src/optimade_maker/archive/utils.py
similarity index 100%
rename from src/optimake/archive/utils.py
rename to src/optimade_maker/archive/utils.py
diff --git a/src/optimake/cli.py b/src/optimade_maker/cli.py
similarity index 93%
rename from src/optimake/cli.py
rename to src/optimade_maker/cli.py
index 6121a66..acbf4c5 100644
--- a/src/optimake/cli.py
+++ b/src/optimade_maker/cli.py
@@ -2,9 +2,9 @@
 
 import click
 
-from optimake.convert import convert_archive
-from optimake.logger import LOGGER
-from optimake.serve import OptimakeServer
+from optimade_maker.convert import convert_archive
+from optimade_maker.logger import LOGGER
+from optimade_maker.serve import OptimakeServer
 
 
 @click.group()
diff --git a/src/optimake/config.py b/src/optimade_maker/config.py
similarity index 100%
rename from src/optimake/config.py
rename to src/optimade_maker/config.py
diff --git a/src/optimake/convert.py b/src/optimade_maker/convert.py
similarity index 100%
rename from src/optimake/convert.py
rename to src/optimade_maker/convert.py
diff --git a/src/optimake/logger.py b/src/optimade_maker/logger.py
similarity index 100%
rename from src/optimake/logger.py
rename to src/optimade_maker/logger.py
diff --git a/src/optimake/parsers.py b/src/optimade_maker/parsers.py
similarity index 98%
rename from src/optimake/parsers.py
rename to src/optimade_maker/parsers.py
index ac428c8..3aa033e 100644
--- a/src/optimake/parsers.py
+++ b/src/optimade_maker/parsers.py
@@ -10,7 +10,7 @@
 from optimade.models import EntryResource
 from pymatgen.entries.computed_entries import ComputedStructureEntry
 
-from optimake.config import PropertyDefinition
+from optimade_maker.config import PropertyDefinition
 
 
 def pybtex_to_optimade(bib_entry: Any, properties=None) -> EntryResource:
diff --git a/src/optimake/serve.py b/src/optimade_maker/serve.py
similarity index 97%
rename from src/optimake/serve.py
rename to src/optimade_maker/serve.py
index 4f880d5..971cfa3 100644
--- a/src/optimake/serve.py
+++ b/src/optimade_maker/serve.py
@@ -6,14 +6,14 @@
 import bson.json_util
 import uvicorn
 
-from optimake.logger import LOGGER
+from optimade_maker.logger import LOGGER
 
 
 def get_optimake_provider_info(index_base_url=None):
     info = {
         "prefix": "optimake",
         "name": "Optimake",
-        "description": "Provider created with optimake",
+        "description": "Provider created with optimade-maker",
         "homepage": "https://github.com/materialscloud-org/optimade-maker",
         "index_base_url": index_base_url,
     }
diff --git a/src/optimake/__init__.py b/src/optimake/__init__.py
deleted file mode 100644
index 9e85e99..0000000
--- a/src/optimake/__init__.py
+++ /dev/null
@@ -1,4 +0,0 @@
-from optimake.config import Config
-from optimake.convert import convert_archive
-
-__all__ = ("Config", "convert_archive")
diff --git a/tests/test_archive.py b/tests/test_archive.py
index c442638..54d5bb3 100644
--- a/tests/test_archive.py
+++ b/tests/test_archive.py
@@ -1,6 +1,6 @@
 import traceback
 
-from optimake.config import UnsupportedConfigVersion
+from optimade_maker.config import UnsupportedConfigVersion
 
 archive_url = "https://staging-archive.materialscloud.org/"
 test_record_id = 1408
@@ -8,7 +8,7 @@
 
 def test_archive_record_metadata():
     """Test ArchiveRecord to read metadata."""
-    from optimake.archive.archive_record import ArchiveRecord
+    from optimade_maker.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 optimake.archive.archive_record import ArchiveRecord
+    from optimade_maker.archive.archive_record import ArchiveRecord
 
     try:
         record = ArchiveRecord(
diff --git a/tests/test_convert.py b/tests/test_convert.py
index a84c1ea..c4ce8ff 100644
--- a/tests/test_convert.py
+++ b/tests/test_convert.py
@@ -5,7 +5,7 @@
 import numpy as np
 import pytest
 from optimade.models import EntryInfoResource
-from optimake.convert import convert_archive
+from optimade_maker.convert import convert_archive
 
 EXAMPLE_ARCHIVES = (Path(__file__).parent.parent / "examples").glob("*")
 
@@ -98,7 +98,7 @@ def check_arrays(reference, test, field):
 def test_unique_id_generator():
     """Unit tests for some common cases of the unique ID generator."""
 
-    from optimake.convert import _set_unique_entry_ids
+    from optimade_maker.convert import _set_unique_entry_ids
 
     entry_ids = [
         "data/structures/1.cif",
diff --git a/tests/test_yaml.py b/tests/test_yaml.py
index 71747ee..65a7e9f 100644
--- a/tests/test_yaml.py
+++ b/tests/test_yaml.py
@@ -1,7 +1,7 @@
 from pathlib import Path
 
 import pytest
-from optimake.config import Config
+from optimade_maker.config import Config
 
 EXAMPLE_YAMLS = (Path(__file__).parent.parent / "examples").glob("*/optimade.yaml")