chore: Use rtd theme (#63)

* doc: use rtd theme

* ci: require that the poetry lock file is up to date (#64)

* ci: require that the poetry lock file is up to date
* refactor: use pathlib in tests
* chore: lock via poetry
* chore: update poetry version to 1.5
* fix: add sphinx_rtd_theme and update lock

---------

Co-authored-by: Matt Stone <matt@fulcrumgenomics.com>

---------

Co-authored-by: Nils Homer <nh13@users.noreply.github.com>

Author: msto

.github/workflows/pythonpackage.yml

@@ -2,7 +2,7 @@ name: Python package
 
 on: [push]
 env:
-  POETRY_VERSION: 1.2
+  POETRY_VERSION: 1.5
 
 jobs:
   testing:
@@ -45,6 +45,11 @@ jobs:
       shell: bash
       run: poetry run pip --version >/dev/null 2>&1 || rm -rf .venv
 
+    - name: Check that the lock file is up to date
+      shell: bash
+      run: |
+        poetry lock --check
+
     - name: Install deps
       shell: bash
       run: |

docs/conf.py

@@ -30,7 +30,8 @@
               'sphinx.ext.todo', 
               'sphinx.ext.ifconfig',
               'sphinx.ext.intersphinx',
-              'sphinx.ext.napoleon']
+              'sphinx.ext.napoleon',
+              'sphinx_rtd_theme']
 
 intersphinx_mapping = {'python': ('http://docs.python.org/3.6', None)}
 
@@ -118,7 +119,7 @@
 
 # The theme to use for HTML and HTML Help pages.  Major themes that come with
 # Sphinx are currently 'default' and 'sphinxdoc'.
-html_theme = 'default'
+html_theme = 'sphinx_rtd_theme'
 
 # Theme options are theme-specific and customize the look and feel of a theme
 # further.  For a list of options available for each theme, see the

fgpyo/fasta/tests/test_builder.py

@@ -4,7 +4,6 @@
 from tempfile import NamedTemporaryFile as NamedTemp
 
 import pytest
-from py._path.local import LocalPath as TmpDir
 from pytest import raises
 
 from fgpyo.fasta.builder import FastaBuilder
@@ -64,14 +63,14 @@ def test_bases_string_from_ContigBuilder_add(
     bases: str,
     times: int,
     expected: str,
-    tmpdir: TmpDir,
+    tmp_path: Path,
 ) -> None:
     """
     Reads bases back from fasta and checks that extra spaces are removed and bases are uppercase
     """
     builder = FastaBuilder()
     builder.add(name).add(bases, times)
-    with NamedTemp(suffix=".fa", dir=tmpdir, mode="w", delete=True) as fp:
+    with NamedTemp(suffix=".fa", dir=tmp_path, mode="w", delete=True) as fp:
         builder.to_file(Path(fp.name))
         with open(fp.name, "r") as read_fp:
             for line in read_fp.readlines():

fgpyo/sam/tests/test_sam.py

@@ -10,7 +10,6 @@
 
 import pysam
 import pytest
-from py._path.local import LocalPath as TmpDir
 from pysam import AlignmentHeader
 
 import fgpyo.sam as sam
@@ -141,10 +140,10 @@ def test_sam_file_open_writing(
     file_type: SamFileType,
     expected_records: List[pysam.AlignedSegment],
     header_dict: AlignmentHeader,
-    tmpdir: TmpDir,
+    tmp_path: Path,
 ) -> None:
     # use header as a keyword argument
-    with NamedTemp(suffix=file_type.extension, dir=tmpdir, mode="w", delete=False) as fp:
+    with NamedTemp(suffix=file_type.extension, dir=tmp_path, mode="w", delete=False) as fp:
         kwargs = {"header": header_dict}
         with sam._pysam_open(
             path=fp.file, open_for_reading=False, file_type=file_type, **kwargs  # type: ignore
@@ -155,11 +154,13 @@ def test_sam_file_open_writing(
 
 
 def test_sam_file_open_writing_header_keyword(
-    expected_records: List[pysam.AlignedSegment], header_dict: AlignmentHeader, tmpdir: TmpDir
+    expected_records: List[pysam.AlignedSegment],
+    header_dict: AlignmentHeader,
+    tmp_path: Path,
 ) -> None:
     # Use SamWriter
     # use header as a keyword argument
-    with NamedTemp(suffix=".sam", dir=tmpdir, mode="w", delete=False) as fp:
+    with NamedTemp(suffix=".sam", dir=tmp_path, mode="w", delete=False) as fp:
         with sam.writer(path=fp.name, header=header_dict, file_type=SamFileType.SAM) as sam_writer:
             for r in expected_records:
                 sam_writer.write(r)

fgpyo/util/tests/test_metric.py

@@ -11,7 +11,6 @@
 
 import attr
 import pytest
-from py._path.local import LocalPath as TmpDir
 
 from fgpyo.util.metric import Metric
 
@@ -139,8 +138,11 @@ class PersonDefault(Metric["PersonDefault"]):
 
 
 @pytest.mark.parametrize("metric", DUMMY_METRICS)
-def test_metric_roundtrip(tmpdir: TmpDir, metric: DummyMetric) -> None:
-    path: Path = Path(tmpdir) / "metrics.txt"
+def test_metric_roundtrip(
+    tmp_path: Path,
+    metric: DummyMetric,
+) -> None:
+    path: Path = tmp_path / "metrics.txt"
 
     DummyMetric.write(path, metric)
     metrics: List[DummyMetric] = list(DummyMetric.read(path=path))
@@ -149,8 +151,8 @@ def test_metric_roundtrip(tmpdir: TmpDir, metric: DummyMetric) -> None:
     assert metrics[0] == metric
 
 
-def test_metrics_roundtrip(tmpdir: TmpDir) -> None:
-    path: Path = Path(tmpdir) / "metrics.txt"
+def test_metrics_roundtrip(tmp_path: Path) -> None:
+    path: Path = tmp_path / "metrics.txt"
 
     DummyMetric.write(path, *DUMMY_METRICS)
     metrics: List[DummyMetric] = list(DummyMetric.read(path=path))
@@ -173,9 +175,9 @@ def test_metrics_roundtrip_gzip(tmp_path: Path) -> None:
     assert metrics == DUMMY_METRICS
 
 
-def test_metrics_read_extra_columns(tmpdir: TmpDir) -> None:
+def test_metrics_read_extra_columns(tmp_path: Path) -> None:
     person = Person(name="Max", age=42)
-    path = Path(tmpdir) / "metrics.txt"
+    path = tmp_path / "metrics.txt"
     with path.open("w") as writer:
         header = Person.header()
         header.append("foo")
@@ -188,9 +190,9 @@ def test_metrics_read_extra_columns(tmpdir: TmpDir) -> None:
         list(Person.read(path=path, ignore_extra_fields=False))
 
 
-def test_metrics_read_missing_optional_columns(tmpdir: TmpDir) -> None:
+def test_metrics_read_missing_optional_columns(tmp_path: Path) -> None:
     person = PersonMaybeAge(name="Max", age=None)
-    path = Path(tmpdir) / "metrics.txt"
+    path = tmp_path / "metrics.txt"
 
     # The "age" column is optional, and not in the file, but that's ok
     with path.open("w") as writer:
@@ -204,9 +206,9 @@ def test_metrics_read_missing_optional_columns(tmpdir: TmpDir) -> None:
         list(PersonMaybeAge.read(path=path))
 
 
-def test_metric_read_missing_column_with_default(tmpdir: TmpDir) -> None:
+def test_metric_read_missing_column_with_default(tmp_path: Path) -> None:
     person = PersonDefault(name="Max")
-    path = Path(tmpdir) / "metrics.txt"
+    path = tmp_path / "metrics.txt"
 
     # The "age" column hs a default, and not in the file, but that's ok
     with path.open("w") as writer: