From ac451814e3fb833cb9c77e65e22bf88777fb67ec Mon Sep 17 00:00:00 2001 From: Alistair Miles Date: Fri, 6 Dec 2024 17:49:44 +0000 Subject: [PATCH 1/2] Refactor unit and integration tests and corresponding github actions (#686) * refactor integration tests * move legacy to integration * move legacy to integration * temporarily disable notebooks * update unit tests * update coverage action * fix job name * fix coverage action * reinstate notebooks * use pip * tidy up linting * wip fix or ignore mypy errors * fix or ignore mypy errors * fix plasmodium tests * fix typing --- .github/workflows/coverage.yml | 13 +- ...legacy_tests.yml => integration_tests.yml} | 21 +- .github/workflows/linting.yml | 18 +- .github/workflows/notebooks.yml | 11 +- .github/workflows/tests.yml | 4 +- malariagen_data/anoph/genome_features.py | 9 +- malariagen_data/anoph/gplt_params.py | 2 +- malariagen_data/anoph/h12.py | 2 +- malariagen_data/anoph/hap_frq.py | 8 +- malariagen_data/anoph/sample_metadata.py | 2 +- malariagen_data/anoph/snp_frq.py | 11 +- malariagen_data/util.py | 1 + poetry.lock | 1466 ++++++++++------- pyproject.toml | 1 + tests/{ => integration}/test_af1.py | 0 tests/{ => integration}/test_ag3.py | 0 tests/{ => integration}/test_amin1.py | 0 .../test_pf7.py} | 0 .../test_pf8.py} | 0 .../test_pv4.py} | 0 tests/test_plasmodium.py | 8 +- tests/test_plasmodium_config.json | 2 +- 22 files changed, 891 insertions(+), 688 deletions(-) rename .github/workflows/{legacy_tests.yml => integration_tests.yml} (75%) rename tests/{ => integration}/test_af1.py (100%) rename tests/{ => integration}/test_ag3.py (100%) rename tests/{ => integration}/test_amin1.py (100%) rename tests/{test_pf7_integration.py => integration/test_pf7.py} (100%) rename tests/{test_pf8_integration.py => integration/test_pf8.py} (100%) rename tests/{test_pv4_integration.py => integration/test_pv4.py} (100%) diff --git a/.github/workflows/coverage.yml b/.github/workflows/coverage.yml index b5e4f3bc5..88d799320 100644 --- a/.github/workflows/coverage.yml +++ b/.github/workflows/coverage.yml @@ -15,20 +15,17 @@ jobs: - name: Checkout source uses: actions/checkout@v4 - - name: Install poetry - run: pipx install poetry==1.8.3 - - name: Setup python uses: actions/setup-python@v5 with: python-version: '3.12' - cache: 'poetry' + cache: 'pip' - - name: Install dependencies - run: poetry install + - name: Install package + run: pip install .[dev] - - name: Run tests with coverage - run: poetry run pytest --durations=20 -v --cov malariagen_data/anoph --cov-report=xml tests/anoph + - name: Run unit tests with coverage + run: pytest -v tests --ignore tests/integration --cov malariagen_data/anoph --cov-report=xml - name: Upload coverage report uses: codecov/codecov-action@v3 diff --git a/.github/workflows/legacy_tests.yml b/.github/workflows/integration_tests.yml similarity index 75% rename from .github/workflows/legacy_tests.yml rename to .github/workflows/integration_tests.yml index 80a392337..7fd65b4c2 100644 --- a/.github/workflows/legacy_tests.yml +++ b/.github/workflows/integration_tests.yml @@ -1,4 +1,4 @@ -name: legacy_tests +name: integration_tests on: push: branches: @@ -7,7 +7,7 @@ on: branches: - master jobs: - legacy_tests: + integration_tests: strategy: fail-fast: true matrix: @@ -23,17 +23,14 @@ jobs: - name: Checkout source uses: actions/checkout@v4 - - name: Install poetry - run: pipx install poetry==1.8.3 - - name: Setup python uses: actions/setup-python@v5 with: python-version: ${{ matrix.python-version }} - cache: "poetry" + cache: "pip" - - name: Install dependencies - run: poetry install + - name: Install package + run: pip install .[dev] - id: 'auth' name: 'Set up Google Cloud authentication' @@ -53,14 +50,14 @@ jobs: uses: actions/cache/restore@v3 with: path: gcs_cache - key: gcs_cache_tests_20240922 + key: gcs_cache_integration_tests_20240922 - - name: Run full test suite - run: poetry run pytest --durations=20 --ignore=tests/anoph -v tests + - name: Run integration tests + run: pytest --durations=20 -v tests/integration - name: Save GCS cache uses: actions/cache/save@v3 if: always() with: path: gcs_cache - key: gcs_cache_tests_20240922 + key: gcs_cache_integration_tests_20240922 diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml index 40ce7d2c0..666c3ea63 100644 --- a/.github/workflows/linting.yml +++ b/.github/workflows/linting.yml @@ -12,13 +12,21 @@ jobs: fail-fast: true runs-on: ubuntu-latest steps: - - uses: actions/checkout@v4 - - uses: actions/setup-python@v5 + - name: Checkout source + uses: actions/checkout@v4 + + - name: Setup python + uses: actions/setup-python@v5 with: python-version: '3.12' - - uses: pre-commit/action@v3.0.0 - - name: Install mypy - run: pip install mypy + cache: 'pip' + + - name: Run pre-commit checks + uses: pre-commit/action@v3.0.0 + + - name: Install package + run: pip install .[dev] + - name: Run mypy run: | mypy malariagen_data tests --ignore-missing-imports diff --git a/.github/workflows/notebooks.yml b/.github/workflows/notebooks.yml index 6900d2db4..c3f8950a1 100644 --- a/.github/workflows/notebooks.yml +++ b/.github/workflows/notebooks.yml @@ -19,17 +19,14 @@ jobs: - name: Checkout source uses: actions/checkout@v4 - - name: Install poetry - run: pipx install poetry==1.8.3 - - name: Setup python uses: actions/setup-python@v5 with: python-version: "3.12" - cache: "poetry" + cache: "pip" - - name: Install dependencies - run: poetry install + - name: Install package + run: pip install .[dev] - id: 'auth' name: 'Set up Google Cloud authentication' @@ -52,7 +49,7 @@ jobs: key: gcs_cache_notebooks_20240922 - name: Run notebooks - run: poetry run jupyter nbconvert --execute notebooks/*.ipynb --inplace + run: jupyter nbconvert --execute notebooks/*.ipynb --inplace - name: Save GCS cache uses: actions/cache/save@v3 diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index b8c1b870e..942aad738 100644 --- a/.github/workflows/tests.yml +++ b/.github/workflows/tests.yml @@ -32,5 +32,5 @@ jobs: - name: Install package run: pip install "${{ matrix.numpy-version }}" .[dev] - - name: Run fast unit tests - run: pytest -v tests/anoph --typeguard-packages=malariagen_data,malariagen_data.anoph + - name: Run unit tests + run: pytest -v tests --ignore tests/integration --typeguard-packages=malariagen_data,malariagen_data.anoph diff --git a/malariagen_data/anoph/genome_features.py b/malariagen_data/anoph/genome_features.py index 99ae82edc..4c1a8b0b3 100644 --- a/malariagen_data/anoph/genome_features.py +++ b/malariagen_data/anoph/genome_features.py @@ -415,11 +415,12 @@ def plot_genes( # Increase the figure height by a certain factor, to accommodate labels. height_increase_factor = 1.3 + assert fig.height is not None fig.height = int(fig.height * height_increase_factor) # Get the original y_range. # Note: fig.y_range is not subscriptable. - orig_y_range = fig.y_range.start, fig.y_range.end + orig_y_range = fig.y_range.start, fig.y_range.end # type: ignore # Determine the midpoint of the original range, to rescale outward from there. orig_mid_y_range = (orig_y_range[0] + orig_y_range[1]) / 2 @@ -432,7 +433,7 @@ def plot_genes( new_y_end = orig_mid_y_range + new_y_range_extent_half # Set the new y_range. - fig.y_range = bokeh.models.Range1d(new_y_start, new_y_end) + fig.y_range = bokeh.models.Range1d(new_y_start, new_y_end) # type: ignore debug("determine midpoint of each gene rectangle") data["mid_x"] = (data["start"] + data["end"]) / 2 @@ -474,7 +475,7 @@ def plot_genes( data_as_cds = bokeh.models.ColumnDataSource(data) # Create a LabelSet for the gene pointers. - gene_pointers_ls = bokeh.models.LabelSet( + gene_pointers_ls = bokeh.models.LabelSet( # type: ignore source=data_as_cds, x="mid_x", y="pointer_y", @@ -486,7 +487,7 @@ def plot_genes( ) # Create a LabelSet for the gene labels. - gene_labels_ls = bokeh.models.LabelSet( + gene_labels_ls = bokeh.models.LabelSet( # type: ignore source=data_as_cds, x="mid_x", y="label_y", diff --git a/malariagen_data/anoph/gplt_params.py b/malariagen_data/anoph/gplt_params.py index 6439d2f23..cf1857d4f 100644 --- a/malariagen_data/anoph/gplt_params.py +++ b/malariagen_data/anoph/gplt_params.py @@ -127,6 +127,6 @@ ] gene_labelset: TypeAlias = Annotated[ - bokeh.models.LabelSet, + bokeh.models.LabelSet, # type: ignore "A LabelSet to use in the plot.", ] diff --git a/malariagen_data/anoph/h12.py b/malariagen_data/anoph/h12.py index fc3df603f..3e211eeb3 100644 --- a/malariagen_data/anoph/h12.py +++ b/malariagen_data/anoph/h12.py @@ -823,7 +823,7 @@ def plot_h12_gwss_multi_panel( figs.append(fig2) # Combine plots into a single figure. - fig = bokeh.layouts.gridplot( + fig = bokeh.layouts.gridplot( # type: ignore figs, ncols=1, toolbar_location="above", diff --git a/malariagen_data/anoph/hap_frq.py b/malariagen_data/anoph/hap_frq.py index 9445f7f00..5dcf6ddb2 100644 --- a/malariagen_data/anoph/hap_frq.py +++ b/malariagen_data/anoph/hap_frq.py @@ -107,7 +107,7 @@ def haplotypes_frequencies( hap_dict.update(f) freq_cols["frq_" + coh] = list(hap_dict.values()) - df_freqs = pd.DataFrame(freq_cols, index=hap_dict.keys()) + df_freqs = pd.DataFrame(freq_cols, index=list(hap_dict.keys())) # Compute max_af. df_max_af = pd.DataFrame({"max_af": df_freqs.max(axis=1)}) @@ -230,14 +230,14 @@ def haplotypes_frequencies_advanced( freq_cols["frq_" + cohort_key_str] = list(hap_freq.values()) nobs_cols["nobs_" + cohort_key_str] = list(hap_nob.values()) - df_freqs = pd.DataFrame(freq_cols, index=hap_freq.keys()) + df_freqs = pd.DataFrame(freq_cols, index=list(hap_freq.keys())) # Compute max_af. df_max_af = pd.DataFrame({"max_af": df_freqs.max(axis=1)}) - df_counts = pd.DataFrame(count_cols, index=hap_count.keys()) + df_counts = pd.DataFrame(count_cols, index=list(hap_count.keys())) - df_nobs = pd.DataFrame(nobs_cols, index=hap_nob.keys()) + df_nobs = pd.DataFrame(nobs_cols, index=list(hap_nob.keys())) # Build the final dataframe. df_haps = pd.concat([df_freqs, df_counts, df_nobs, df_max_af], axis=1) diff --git a/malariagen_data/anoph/sample_metadata.py b/malariagen_data/anoph/sample_metadata.py index 56f2aabac..3088508ba 100644 --- a/malariagen_data/anoph/sample_metadata.py +++ b/malariagen_data/anoph/sample_metadata.py @@ -1270,7 +1270,7 @@ def cohorts( df_cohorts = pd.read_csv(f, sep=",", na_values="") # Ensure all column names are lower case. - df_cohorts.columns = [c.lower() for c in df_cohorts.columns] + df_cohorts.columns = [c.lower() for c in df_cohorts.columns] # type: ignore return df_cohorts diff --git a/malariagen_data/anoph/snp_frq.py b/malariagen_data/anoph/snp_frq.py index ae4a46b9f..cd5304d7b 100644 --- a/malariagen_data/anoph/snp_frq.py +++ b/malariagen_data/anoph/snp_frq.py @@ -614,7 +614,7 @@ def snp_allele_frequencies_advanced( # Apply variant query. if variant_query is not None: - loc_variants = df_variants.eval(variant_query).values + loc_variants = np.asarray(df_variants.eval(variant_query)) # Check for no SNPs remaining after applying variant query. if np.count_nonzero(loc_variants) == 0: @@ -1192,8 +1192,8 @@ def plot_frequencies_interactive_map( # Set up interactive controls. variants = ds["variant_label"].values - taxa = ds["cohort_taxon"].to_pandas().dropna().unique() - periods = ds["cohort_period"].to_pandas().dropna().unique() + taxa = ds["cohort_taxon"].to_pandas().dropna().unique() # type: ignore + periods = ds["cohort_period"].to_pandas().dropna().unique() # type: ignore controls = ipywidgets.interactive( self.plot_frequencies_map_markers, m=ipywidgets.fixed(freq_map), @@ -1281,7 +1281,10 @@ def snp_genotype_allele_counts( loc_sites = df_snps[f"pass_{site_mask}"] df_snps = df_snps.loc[loc_sites] - return df_snps.query(snp_query) + if snp_query is not None: + df_snps = df_snps.query(snp_query) + + return df_snps @numba.jit(nopython=True) diff --git a/malariagen_data/util.py b/malariagen_data/util.py index 0e6d28322..81ed4733d 100644 --- a/malariagen_data/util.py +++ 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lock-version = "2.0" python-versions = ">=3.10,<3.13" -content-hash = "91f11922fd7ceab43591ab19b88894cc233f398c3410bdce0de4dfaa41b6ae15" +content-hash = "ff3553dca67a90cb5a7ef7f08d57c58a1deae4210083eaf7f950760973b58312" diff --git a/pyproject.toml b/pyproject.toml index 10c460564..9dd2fb68e 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -29,6 +29,7 @@ dask = {version="*", extras=["array"]} distributed = "*" fsspec = "*" gcsfs = "*" +s3fs = "*" google-auth = "*" BioPython = "*" scikit-allel = ">=1.3.13" diff --git a/tests/test_af1.py b/tests/integration/test_af1.py similarity index 100% rename from tests/test_af1.py rename to tests/integration/test_af1.py diff --git a/tests/test_ag3.py b/tests/integration/test_ag3.py similarity index 100% rename from tests/test_ag3.py rename to tests/integration/test_ag3.py diff --git a/tests/test_amin1.py b/tests/integration/test_amin1.py similarity index 100% rename from tests/test_amin1.py rename to tests/integration/test_amin1.py diff --git a/tests/test_pf7_integration.py b/tests/integration/test_pf7.py similarity index 100% rename from tests/test_pf7_integration.py rename to tests/integration/test_pf7.py diff --git a/tests/test_pf8_integration.py b/tests/integration/test_pf8.py similarity index 100% rename from tests/test_pf8_integration.py rename to tests/integration/test_pf8.py diff --git a/tests/test_pv4_integration.py b/tests/integration/test_pv4.py similarity index 100% rename from tests/test_pv4_integration.py rename to tests/integration/test_pv4.py diff --git a/tests/test_plasmodium.py b/tests/test_plasmodium.py index 8bfadd6b1..21676ac48 100644 --- a/tests/test_plasmodium.py +++ b/tests/test_plasmodium.py @@ -186,7 +186,7 @@ def test_setup_returns_config_correctly(self): self.assertEqual( plasmodium.CONF, { - "default_url": "gs://test_plasmodium_release/", + "default_url": "s3://test_plasmodium_release/", "metadata_path": "metadata/test_metadata.txt", "reference_path": "reference/plasmodium.genome.zarr", "reference_contigs": ["contig1", "contig2", "contig3"], @@ -225,10 +225,8 @@ def test_setup_returns_config_correctly(self): @patch("malariagen_data.plasmodium.PlasmodiumDataResource._load_config") def test_setup_overrides_default_url(self, mock_load_config): - url_starts_with_gs = "gs://test_url" - plasmodium = PlasmodiumDataResource( - self.test_config_path, url=url_starts_with_gs - ) + url_override = "s3://test_url" + plasmodium = PlasmodiumDataResource(self.test_config_path, url=url_override) self.assertEqual(plasmodium._path, "test_url") mock_load_config.assert_called_once_with(self.test_config_path) diff --git a/tests/test_plasmodium_config.json b/tests/test_plasmodium_config.json index c82d52264..2b3ff244a 100644 --- a/tests/test_plasmodium_config.json +++ b/tests/test_plasmodium_config.json @@ -1,5 +1,5 @@ { - "default_url": "gs://test_plasmodium_release/", + "default_url": "s3://test_plasmodium_release/", "metadata_path": "metadata/test_metadata.txt", "reference_path": "reference/plasmodium.genome.zarr", "reference_contigs": ["contig1", "contig2", "contig3"], From 70ad53d69bb1f6425fc048c8b10fb9e91b20775b Mon Sep 17 00:00:00 2001 From: Jon Brenas <51911846+jonbrenas@users.noreply.github.com> Date: Fri, 6 Dec 2024 17:52:33 +0000 Subject: [PATCH 2/2] Added the option for a palette (#688) --- malariagen_data/anoph/cnv_data.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/malariagen_data/anoph/cnv_data.py b/malariagen_data/anoph/cnv_data.py index 219a4493c..23eeef33b 100644 --- a/malariagen_data/anoph/cnv_data.py +++ b/malariagen_data/anoph/cnv_data.py @@ -857,6 +857,7 @@ def plot_cnv_hmm_heatmap_track( width: gplt_params.width = gplt_params.width_default, row_height: gplt_params.row_height = 7, height: Optional[gplt_params.height] = None, + palette: Optional[gplt_params.colors] = cnv_params.colorscale_default, show: gplt_params.show = True, output_backend: gplt_params.output_backend = gplt_params.output_backend_default, ) -> gplt_params.optional_figure: @@ -929,7 +930,6 @@ def plot_cnv_hmm_heatmap_track( ) debug("set up palette and color mapping") - palette = cnv_params.colorscale_default color_mapper = bkmod.LinearColorMapper(low=-1.5, high=4.5, palette=palette) debug("plot the HMM copy number data as an image") @@ -999,6 +999,7 @@ def plot_cnv_hmm_heatmap( width: gplt_params.width = gplt_params.width_default, row_height: gplt_params.row_height = 7, track_height: Optional[gplt_params.track_height] = None, + palette: Optional[gplt_params.colors] = cnv_params.colorscale_default, genes_height: gplt_params.genes_height = gplt_params.genes_height_default, show: gplt_params.show = True, gene_labels: Optional[gplt_params.gene_labels] = None, @@ -1020,6 +1021,7 @@ def plot_cnv_hmm_heatmap( width=width, row_height=row_height, height=track_height, + palette=palette, show=False, ) fig1.xaxis.visible = False