Merge pull request #380 from monarch-initiative/release-0.x

Release v0.8.0
monarch-initiative · Dec 11, 2024 · f9fe293 · f9fe293
2 parents 0abc3aa + dcb6d04
commit f9fe293
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diff --git a/.flake8 b/.flake8
diff --git a/.github/workflows/python_ci.yml b/.github/workflows/python_ci.yml
@@ -20,10 +20,6 @@ jobs:
           with:
             python-version: ${{ matrix.python-version }}
         - name: Install package
-          run: |
-            python3 -m pip install --editable .[test]
+          run: python3 -m pip install --editable .[test]
         - name: Run pytest tests
-          run: |
-            export MPLBACKEND=Agg
-            export GPSEA_CACHEDIR=.gpsea_ci_cachedir
-            pytest
+          run: MPLBACKEND=Agg GPSEA_CACHEDIR=.gpsea_ci_cachedir pytest
diff --git a/.gitignore b/.gitignore
@@ -151,3 +151,6 @@ dmypy.json
 
 # Pyre type checker
 .pyre/
+
+# Ruff (linter & formatter)
+.ruff_cache/
diff --git a/.gpsea_ci_cachedir/protein_cache/NP_852259.1.json b/.gpsea_ci_cachedir/protein_cache/NP_852259.1.json
@@ -0,0 +1,57 @@
+{
+  "protein_id": "NP_852259.1",
+  "label": "T-box transcription factor TBX5",
+  "protein_features": [
+    {
+      "info": {
+        "name": "T-box",
+        "region": {
+          "start": 58,
+          "end": 238
+        }
+      },
+      "feature_type": "DNA_BINDING"
+    },
+    {
+      "info": {
+        "name": "Disordered",
+        "region": {
+          "start": 1,
+          "end": 46
+        }
+      },
+      "feature_type": "REGION"
+    },
+    {
+      "info": {
+        "name": "Disordered",
+        "region": {
+          "start": 250,
+          "end": 356
+        }
+      },
+      "feature_type": "REGION"
+    },
+    {
+      "info": {
+        "name": "Polar residues",
+        "region": {
+          "start": 263,
+          "end": 299
+        }
+      },
+      "feature_type": "COMPOSITIONAL_BIAS"
+    },
+    {
+      "info": {
+        "name": "Basic and acidic residues",
+        "region": {
+          "start": 320,
+          "end": 346
+        }
+      },
+      "feature_type": "COMPOSITIONAL_BIAS"
+    }
+  ],
+  "protein_length": 518
+}
diff --git a/.gpsea_ci_cachedir/protein_cache/NP_852259.1.pickle b/.gpsea_ci_cachedir/protein_cache/NP_852259.1.pickle
diff --git a/.gpsea_ci_cachedir/tx_cache/NM_181486.4.json b/.gpsea_ci_cachedir/tx_cache/NM_181486.4.json
@@ -0,0 +1,127 @@
+{
+  "identifier": "NM_181486.4",
+  "region": {
+    "start": 18869165,
+    "end": 18921399,
+    "contig": {
+      "name": "12",
+      "genbank_acc": "CM000674.2",
+      "refseq_name": "NC_000012.12",
+      "ucsc_name": "chr12",
+      "length": 133275309
+    },
+    "strand": "NEGATIVE"
+  },
+  "exons": [
+    {
+      "start": 18869165,
+      "end": 18869682,
+      "contig": {
+        "name": "12",
+        "genbank_acc": "CM000674.2",
+        "refseq_name": "NC_000012.12",
+        "ucsc_name": "chr12",
+        "length": 133275309
+      },
+      "strand": "NEGATIVE"
+    },
+    {
+      "start": 18871373,
+      "end": 18871558,
+      "contig": {
+        "name": "12",
+        "genbank_acc": "CM000674.2",
+        "refseq_name": "NC_000012.12",
+        "ucsc_name": "chr12",
+        "length": 133275309
+      },
+      "strand": "NEGATIVE"
+    },
+    {
+      "start": 18873389,
+      "end": 18873484,
+      "contig": {
+        "name": "12",
+        "genbank_acc": "CM000674.2",
+        "refseq_name": "NC_000012.12",
+        "ucsc_name": "chr12",
+        "length": 133275309
+      },
+      "strand": "NEGATIVE"
+    },
+    {
+      "start": 18875677,
+      "end": 18875797,
+      "contig": {
+        "name": "12",
+        "genbank_acc": "CM000674.2",
+        "refseq_name": "NC_000012.12",
+        "ucsc_name": "chr12",
+        "length": 133275309
+      },
+      "strand": "NEGATIVE"
+    },
+    {
+      "start": 18876589,
+      "end": 18876737,
+      "contig": {
+        "name": "12",
+        "genbank_acc": "CM000674.2",
+        "refseq_name": "NC_000012.12",
+        "ucsc_name": "chr12",
+        "length": 133275309
+      },
+      "strand": "NEGATIVE"
+    },
+    {
+      "start": 18880416,
+      "end": 18880569,
+      "contig": {
+        "name": "12",
+        "genbank_acc": "CM000674.2",
+        "refseq_name": "NC_000012.12",
+        "ucsc_name": "chr12",
+        "length": 133275309
+      },
+      "strand": "NEGATIVE"
+    },
+    {
+      "start": 18889742,
+      "end": 18889834,
+      "contig": {
+        "name": "12",
+        "genbank_acc": "CM000674.2",
+        "refseq_name": "NC_000012.12",
+        "ucsc_name": "chr12",
+        "length": 133275309
+      },
+      "strand": "NEGATIVE"
+    },
+    {
+      "start": 18908918,
+      "end": 18909145,
+      "contig": {
+        "name": "12",
+        "genbank_acc": "CM000674.2",
+        "refseq_name": "NC_000012.12",
+        "ucsc_name": "chr12",
+        "length": 133275309
+      },
+      "strand": "NEGATIVE"
+    },
+    {
+      "start": 18919203,
+      "end": 18921399,
+      "contig": {
+        "name": "12",
+        "genbank_acc": "CM000674.2",
+        "refseq_name": "NC_000012.12",
+        "ucsc_name": "chr12",
+        "length": 133275309
+      },
+      "strand": "NEGATIVE"
+    }
+  ],
+  "cds_start": 18871411,
+  "cds_end": 18919778
+}
diff --git a/.gpsea_ci_cachedir/variant_cache/12_114355723_114355723_G_A.json b/.gpsea_ci_cachedir/variant_cache/12_114355723_114355723_G_A.json
@@ -0,0 +1,56 @@
+[
+  {
+    "gene_id": "TBX5",
+    "transcript_id": "NM_000192.3",
+    "hgvs_cdna": "NM_000192.3:c.1366G>A",
+    "is_preferred": false,
+    "variant_effects": [
+      "STOP_GAINED"
+    ],
+    "overlapping_exons": [
+      9
+    ],
+    "protein_id": "NP_000183.2",
+    "hgvsp": "NP_000183.2:p.Gln456Ter",
+    "protein_effect_location": {
+      "start": 455,
+      "end": 456
+    }
+  },
+  {
+    "gene_id": "TBX5",
+    "transcript_id": "NM_080717.4",
+    "hgvs_cdna": "NM_080717.4:c.1216C>T",
+    "is_preferred": false,
+    "variant_effects": [
+      "STOP_GAINED"
+    ],
+    "overlapping_exons": [
+      8
+    ],
+    "protein_id": "NP_542448.1",
+    "hgvsp": "NP_542448.1:p.Gln406Ter",
+    "protein_effect_location": {
+      "start": 405,
+      "end": 406
+    }
+  },
+  {
+    "gene_id": "TBX5",
+    "transcript_id": "NM_181486.4",
+    "hgvs_cdna": "NM_181486.4:c.1366C>T",
+    "is_preferred": true,
+    "variant_effects": [
+      "STOP_GAINED"
+    ],
+    "overlapping_exons": [
+      9
+    ],
+    "protein_id": "NP_852259.1",
+    "hgvsp": "NP_852259.1:p.Gln456Ter",
+    "protein_effect_location": {
+      "start": 455,
+      "end": 456
+    }
+  }
+]
diff --git a/.gpsea_ci_cachedir/variant_cache/12_114355723_114355723_G_A.pickle b/.gpsea_ci_cachedir/variant_cache/12_114355723_114355723_G_A.pickle
diff --git a/.gpsea_ci_cachedir/variant_cache/12_114355755_114355756_TG_T.json b/.gpsea_ci_cachedir/variant_cache/12_114355755_114355756_TG_T.json
@@ -0,0 +1,56 @@
+[
+  {
+    "gene_id": "TBX5",
+    "transcript_id": "NM_000192.3",
+    "hgvs_cdna": "NM_000192.3:c.1333del",
+    "is_preferred": false,
+    "variant_effects": [
+      "FRAMESHIFT_VARIANT"
+    ],
+    "overlapping_exons": [
+      9
+    ],
+    "protein_id": "NP_000183.2",
+    "hgvsp": "NP_000183.2:p.His445MetfsTer137",
+    "protein_effect_location": {
+      "start": 444,
+      "end": 445
+    }
+  },
+  {
+    "gene_id": "TBX5",
+    "transcript_id": "NM_080717.4",
+    "hgvs_cdna": "NM_080717.4:c.1183del",
+    "is_preferred": false,
+    "variant_effects": [
+      "FRAMESHIFT_VARIANT"
+    ],
+    "overlapping_exons": [
+      8
+    ],
+    "protein_id": "NP_542448.1",
+    "hgvsp": "NP_542448.1:p.His395MetfsTer137",
+    "protein_effect_location": {
+      "start": 394,
+      "end": 395
+    }
+  },
+  {
+    "gene_id": "TBX5",
+    "transcript_id": "NM_181486.4",
+    "hgvs_cdna": "NM_181486.4:c.1333del",
+    "is_preferred": true,
+    "variant_effects": [
+      "FRAMESHIFT_VARIANT"
+    ],
+    "overlapping_exons": [
+      9
+    ],
+    "protein_id": "NP_852259.1",
+    "hgvsp": "NP_852259.1:p.His445MetfsTer137",
+    "protein_effect_location": {
+      "start": 444,
+      "end": 445
+    }
+  }
+]
diff --git a/.gpsea_ci_cachedir/variant_cache/12_114355755_114355756_TG_T.pickle b/.gpsea_ci_cachedir/variant_cache/12_114355755_114355756_TG_T.pickle
diff --git a/.gpsea_ci_cachedir/variant_cache/12_114355784_114355785_CA_C.json b/.gpsea_ci_cachedir/variant_cache/12_114355784_114355785_CA_C.json
@@ -0,0 +1,56 @@
+[
+  {
+    "gene_id": "TBX5",
+    "transcript_id": "NM_000192.3",
+    "hgvs_cdna": "NM_000192.3:c.1304del",
+    "is_preferred": false,
+    "variant_effects": [
+      "FRAMESHIFT_VARIANT"
+    ],
+    "overlapping_exons": [
+      9
+    ],
+    "protein_id": "NP_000183.2",
+    "hgvsp": "NP_000183.2:p.Leu435ArgfsTer147",
+    "protein_effect_location": {
+      "start": 434,
+      "end": 435
+    }
+  },
+  {
+    "gene_id": "TBX5",
+    "transcript_id": "NM_080717.4",
+    "hgvs_cdna": "NM_080717.4:c.1154del",
+    "is_preferred": false,
+    "variant_effects": [
+      "FRAMESHIFT_VARIANT"
+    ],
+    "overlapping_exons": [
+      8
+    ],
+    "protein_id": "NP_542448.1",
+    "hgvsp": "NP_542448.1:p.Leu385ArgfsTer147",
+    "protein_effect_location": {
+      "start": 384,
+      "end": 385
+    }
+  },
+  {
+    "gene_id": "TBX5",
+    "transcript_id": "NM_181486.4",
+    "hgvs_cdna": "NM_181486.4:c.1304del",
+    "is_preferred": true,
+    "variant_effects": [
+      "FRAMESHIFT_VARIANT"
+    ],
+    "overlapping_exons": [
+      9
+    ],
+    "protein_id": "NP_852259.1",
+    "hgvsp": "NP_852259.1:p.Leu435ArgfsTer147",
+    "protein_effect_location": {
+      "start": 434,
+      "end": 435
+    }
+  }
+]
diff --git a/.gpsea_ci_cachedir/variant_cache/12_114355784_114355785_CA_C.pickle b/.gpsea_ci_cachedir/variant_cache/12_114355784_114355785_CA_C.pickle