more

.github/workflows/checks.yml

@@ -25,7 +25,7 @@ jobs:
           python-version: ${{ matrix.python-version }}
 
       - name: Install dependencies
-        run: python3 -m pip instlall ".[test]"
+        run: python3 -m pip install ".[test]"
 
       - name: Run tests
         run: python3 -m pytest tests/

README.md

@@ -1,3 +1,27 @@
 # WagsTails
 
-Data acquisition tools for Wagnerds
+Data acquisition tools for Wagnerds.
+
+## Installation
+
+Install from PyPI:
+
+```shell
+python3 -m pip install wagstails
+```
+
+## Usage
+
+Data source classes provide a `get_latest()` method that acquires the most recent available data file and returns a pathlib.Path object with its location:
+
+```pycon
+>>> from wagstails.mondo import MondoData
+>>> m = MondoData()
+>>> m.get_latest(force_refresh=True)
+Downloading mondo.owl: 100%|█████████████████| 171M/171M [00:28<00:00, 6.23MB/s]
+PosixPath('/Users/genomicmedlab/.local/share/wagstails/mondo/mondo_v2023-09-12.owl')
+```
+
+## Configuration
+
+All data is stored within source-specific subdirectories of a designated WagsTails data directory. By default, this location is `~/.local/share/wagstails/`, but it can be configured by passing a Path directly to a data class on initialization, via the `$WAGSTAILS` environment variable, or via [XDG data environment variables](https://specifications.freedesktop.org/basedir-spec/basedir-spec-0.6.html).

pyproject.toml

@@ -36,7 +36,6 @@ dev = ["pre-commit", "black", "ruff"]
 
 [project.urls]
 Homepage = "https://github.com/GenomicMedLab/WagsTails/"
-# Documentation = ""
 Changelog = "https://github.com/GenomicMedLab/WagsTails/releases"
 Source = "https://github.com/GenomicMedLab/WagsTails/"
 "Bug Tracker" = "https://github.com/GenomicMedLab/WagsTails/issues"

src/wagstails/__init__.py

@@ -1 +1,5 @@
 """Data acquisition tools for Wagnerds."""
+from .chembl import ChemblData
+from .mondo import MondoData
+
+__all__ = ["MondoData", "ChemblData"]

src/wagstails/base_source.py

@@ -36,7 +36,13 @@ def __init__(self, data_dir: Optional[Path] = None, silent: bool = True) -> None
             data_dir = self._get_data_base() / self._src_name
         data_dir.mkdir(exist_ok=True)
         self._data_dir = data_dir
-        self._tqdm_params = {"unit": "B", "ncols": 80, "disable": silent}
+        self._tqdm_params = {
+            "unit": "B",
+            "ncols": 80,
+            "disable": silent,
+            "unit_divisor": 1024,
+            "unit_scale": True,
+        }
 
     @abc.abstractmethod
     def get_latest(self, from_local: bool = False, force_refresh: bool = False) -> Path:

src/wagstails/chembl.py

@@ -12,7 +12,7 @@
 class ChemblData(DataSource):
     """Provide access to ChEMBL database."""
 
-    def __init__(self, data_dir: Optional[Path] = None, silent: bool = True) -> None:
+    def __init__(self, data_dir: Optional[Path] = None, silent: bool = False) -> None:
         """Set common class parameters.
 
         :param data_dir: direct location to store data files in. If not provided, tries

src/wagstails/mondo.py

@@ -10,7 +10,7 @@
 class MondoData(GitHubDataSource):
     """Provide access to Mondo disease ontology data."""
 
-    def __init__(self, data_dir: Optional[Path] = None, silent: bool = True) -> None:
+    def __init__(self, data_dir: Optional[Path] = None, silent: bool = False) -> None:
         """Set common class parameters.
 
         :param data_dir: direct location to store data files in. If not provided, tries

tests/test_chembl.py

@@ -19,7 +19,7 @@ def chembl_data_dir(base_data_dir: Path):
 @pytest.fixture(scope="function")
 def chembl(chembl_data_dir: Path):
     """Provide ChemblData fixture"""
-    return ChemblData(chembl_data_dir)
+    return ChemblData(chembl_data_dir, silent=True)
 
 
 @pytest.fixture(scope="module")

tests/test_mondo.py

@@ -21,7 +21,7 @@ def mondo_data_dir(base_data_dir: Path):
 @pytest.fixture(scope="function")
 def mondo(mondo_data_dir: Path):
     """Provide MondoData fixture"""
-    return MondoData(mondo_data_dir)
+    return MondoData(mondo_data_dir, silent=True)
 
 
 @pytest.fixture(scope="module")