bioversions 0.5.376__py3-none-any.whl → 0.7.1__py3-none-any.whl

bioversions/__init__.py

@@ -1,5 +1,9 @@
-# -*- coding: utf-8 -*-
-
 """What's the current version for each biological database?"""  # noqa:D400
 
-from .sources import get_rows, get_version, resolve  # noqa:F401
+from .sources import get_rows, get_version, resolve
+
+__all__ = [
+    "get_rows",
+    "get_version",
+    "resolve",
+]

bioversions/__main__.py

@@ -1,5 +1,3 @@
-# -*- coding: utf-8 -*-
-
 """Command line interface for bioversions."""
 
 from .cli import main

bioversions/charts.py

@@ -1,5 +1,3 @@
-# -*- coding: utf-8 -*-
-
 """Generation of charts summarizing bioversions."""
 
 import os
@@ -21,7 +19,7 @@ def version_types_pie_chart():
         "Missing" if getter.version_type is None else getter.version_type.value
         for getter in get_getters()
     )
-    labels, counts = zip(*counts.most_common())
+    labels, counts = zip(*counts.most_common(), strict=False)
     fig, ax = plt.subplots()
     ax.pie(
         counts,
@@ -29,9 +27,7 @@ def version_types_pie_chart():
         autopct="%1.f%%",
         startangle=30,
         explode=[0.01 for _ in range(len(counts))],
-        # shadow=True,
     )
-    # fig.legend(fontsize='medium')
     fig.tight_layout()
     path = os.path.join(IMG, "version_types.svg")
     plt.savefig(path, dpi=300)
@@ -45,7 +41,7 @@ def verioning_date_formats_pie_chart():
         for getter in get_getters()
         if getter.version_type in {VersionType.date, VersionType.month}
     )
-    labels, counts = zip(*counts.most_common())
+    labels, counts = zip(*counts.most_common(), strict=False)
     fig, ax = plt.subplots()
     ax.pie(
         counts,
@@ -67,7 +63,7 @@ def has_release_url():
         for getter in get_getters()
         if getter.version_type != VersionType.unversioned
     )
-    labels, counts = zip(*counts.most_common())
+    labels, counts = zip(*counts.most_common(), strict=False)
     fig, ax = plt.subplots()
     ax.pie(
         counts,

bioversions/cli.py

@@ -1,5 +1,3 @@
-# -*- coding: utf-8 -*-
-
 """Command line interface for bioversions."""
 
 import click
@@ -21,9 +19,9 @@ main.add_command(update)
 web = make_web_command(
     app="bioversions.wsgi:app",
     group=main,
-    command_kwargs=dict(
-        help="Run the bioversions web application.",
-    ),
+    command_kwargs={
+        "help": "Run the bioversions web application.",
+    },
 )
 
 

bioversions/resources/__init__.py

@@ -1,5 +1,3 @@
-# -*- coding: utf-8 -*-
-
 """Resources."""
 
 import datetime
@@ -9,17 +7,18 @@ from pathlib import Path
 import yaml
 
 __all__ = [
-    "VERSIONS_PATH",
     "EXPORT_PATH",
+    "VERSIONS_PATH",
     "load_versions",
-    "write_versions",
     "write_export",
+    "write_versions",
 ]
 
 HERE = Path(__file__).parent.resolve()
 VERSIONS_PATH = HERE.joinpath(HERE, "versions.json")
 
 ROOT = HERE.parent.parent.parent.resolve()
+PYPROJECT_TOML_PATH = ROOT.joinpath("pyproject.toml")
 DOCS = ROOT.joinpath("docs")
 EXPORTS_DIRECTORY = DOCS.joinpath("_data")
 EXPORT_PATH = EXPORTS_DIRECTORY.joinpath("versions.yml")
@@ -28,22 +27,34 @@ FAILURES_PATH = DOCS.joinpath("failures.md")
 
 def load_versions():
     """Load Bioversions data."""
+    if not VERSIONS_PATH.is_file():
+        raise RuntimeError(
+            f"bioversions was not packaged/built/installed properly -"
+            f"{VERSIONS_PATH.name} was not found inside the distribution"
+        )
     with open(VERSIONS_PATH) as file:
         return json.load(file)
 
 
 def _date_converter(o):
-    if isinstance(o, (datetime.datetime, datetime.date)):
+    if isinstance(o, datetime.datetime | datetime.date):
         return o.strftime("%Y-%m-%d")
 
 
-def write_versions(versions, indent: int = 2, **kwargs):
+def write_versions(versions, indent: int = 2, **kwargs) -> None:
     """Write Bioversions data."""
+    _ensure_editable()
     with open(VERSIONS_PATH, "w") as file:
         json.dump(versions, file, indent=indent, default=_date_converter, **kwargs)
 
 
-def write_export(versions):
+def write_export(versions) -> None:
     """Write Bioversions data to the export directory."""
+    _ensure_editable()
     with open(EXPORT_PATH, "w") as file:
         yaml.safe_dump(versions, file)
+
+
+def _ensure_editable() -> None:
+    if not PYPROJECT_TOML_PATH.is_file():
+        raise RuntimeError("can not make export when bioversions is not installed in editable mode")

bioversions/resources/update.py

@@ -1,5 +1,3 @@
-# -*- coding: utf-8 -*-
-
 """Update the web page."""
 
 import getpass
@@ -7,6 +5,7 @@ import sys
 from datetime import datetime
 
 import click
+from tqdm import tqdm
 from tqdm.contrib.logging import logging_redirect_tqdm
 
 from bioversions.resources import (
@@ -16,7 +15,7 @@ from bioversions.resources import (
     write_export,
     write_versions,
 )
-from bioversions.sources import _iter_versions
+from bioversions.sources import FailureTuple, _iter_versions
 from bioversions.version import get_git_hash
 
 __all__ = [
@@ -36,7 +35,7 @@ def update(force: bool):
         _update(force=force)
 
 
-def _update(force: bool):
+def _update(force: bool):  # noqa:C901
     if not get_git_hash():
         click.secho("Not on development installation", fg="red")
         return sys.exit(1)
@@ -49,10 +48,10 @@ def _update(force: bool):
     today = datetime.now().strftime("%Y-%m-%d")
 
     changes = False
-    errors = []
-    for bv, error in _iter_versions(use_tqdm=True):
-        if error is not None or bv is None:
-            errors.append(error)
+    failure_tuples = []
+    for bv in _iter_versions(use_tqdm=True):
+        if isinstance(bv, FailureTuple):
+            failure_tuples.append(bv)
             continue
 
         if bv.name in versions:
@@ -83,7 +82,7 @@ def _update(force: bool):
             v["releases"].append(append_dict)
 
     if not changes and not force:
-        click.secho(f"No changes to {EXPORT_PATH}", fg="yellow", bold=True)
+        tqdm.write(click.style(f"No changes to {EXPORT_PATH}", fg="yellow", bold=True))
     else:
         rv_database = sorted(versions.values(), key=lambda version: version["name"].lower())
         rv = {
@@ -94,11 +93,20 @@ def _update(force: bool):
             },
             "database": rv_database,
         }
-        click.secho(f"Writing new {EXPORT_PATH}", fg="green", bold=True)
+        tqdm.write(click.style(f"Writing new {EXPORT_PATH}", fg="green", bold=True))
         write_export(rv)
         write_versions(rv)
 
-    FAILURES_PATH.write_text("# Errors\n\n" + "\n".join(f"- {error}" for error in errors))
+    if failure_tuples:
+        click.secho(f"Writing failure summary to {FAILURES_PATH}")
+        text = "# Summary of Errors\n\n"
+        for t in failure_tuples:
+            text += f"- {t.name} - {t.message}\n"
+        text += "\n"
+        for t in failure_tuples:
+            text += f"## {t.name}\n\nUsing class: `{t.clstype}`\n\n"
+            text += f"```python-traceback\n{t.trace}\n```\n\n"
+        FAILURES_PATH.write_text(text)
 
 
 def _log_update(bv) -> None:
@@ -106,7 +114,7 @@ def _log_update(bv) -> None:
     if bv.homepage:
         text += f". See {bv.homepage}"
 
-    click.secho(text, fg="green", bold=True)
+    tqdm.write(click.style(text, fg="green", bold=True))
 
     try:
         from .. import slack_client