Merge branch 'main' into dev

pachterlab · May 2, 2023 · f76488f · f76488f
2 parents 39de9bf + fe845f2
commit f76488f
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Showing 5 changed files with 7 additions and 50 deletions.
diff --git a/README.md b/README.md
@@ -1,7 +1,8 @@
 # gget
 [![pypi version](https://img.shields.io/pypi/v/gget)](https://pypi.org/project/gget)
 [![image](https://anaconda.org/bioconda/gget/badges/version.svg)](https://anaconda.org/bioconda/gget)
-[![Downloads](https://static.pepy.tech/personalized-badge/gget?period=total&units=international_system&left_color=grey&right_color=brightgreen&left_text=Downloads)](https://pepy.tech/project/gget)
+[![Downloads](https://static.pepy.tech/personalized-badge/gget?period=total&units=international_system&left_color=grey&right_color=brightgreen&left_text=downloads)](https://pepy.tech/project/gget)
+[![Conda](https://img.shields.io/conda/dn/bioconda/gget?logo=Anaconda)](https://anaconda.org/bioconda/gget)
 [![license](https://img.shields.io/pypi/l/gget)](LICENSE)
 ![status](https://github.com/pachterlab/gget/workflows/CI/badge.svg)
 ![status](https://github.com/lauraluebbert/test_gget_alphafold/workflows/CI_alphafold/badge.svg)

diff --git a/docs/src/introduction.md b/docs/src/introduction.md
@@ -1,6 +1,7 @@
 [![pypi version](https://img.shields.io/pypi/v/gget)](https://pypi.org/project/gget)
 [![image](https://anaconda.org/bioconda/gget/badges/version.svg)](https://anaconda.org/bioconda/gget)
 [![Downloads](https://static.pepy.tech/personalized-badge/gget?period=total&units=international_system&left_color=grey&right_color=brightgreen&left_text=Downloads)](https://pepy.tech/project/gget)
+[![Conda](https://img.shields.io/conda/dn/bioconda/gget?logo=Anaconda)](https://anaconda.org/bioconda/gget)
 [![license](https://img.shields.io/pypi/l/gget)](LICENSE)
 ![status](https://github.com/pachterlab/gget/workflows/CI/badge.svg)
 ![status](https://github.com/lauraluebbert/test_gget_alphafold/workflows/CI_alphafold/badge.svg)

diff --git a/tests/fixtures/test_blast.json b/tests/fixtures/test_blast.json
@@ -14,7 +14,7 @@
                 222,
                 222,
                 "100%",
-                7.999999999999999e-54,
+                9e-54,
                 "100.00%",
                 67524,
                 "NG_029005.2"
@@ -37,7 +37,7 @@
                 "Max Score": 222,
                 "Total Score": 222,
                 "Query Cover": "100%",
-                "E value": 8e-54,
+                "E value": 9e-54,
                 "Per. Ident": "100.00%",
                 "Acc. Len": 67524,
                 "Accession": "NG_029005.2"

diff --git a/tests/fixtures/test_pdb.json b/tests/fixtures/test_pdb.json
@@ -6650,52 +6650,6 @@
                 "recvd_initial_deposition_date": "1984-03-07T00:00:00+0000",
                 "status_code": "REL"
             },
-            "pdbx_vrpt_summary": {
-                "pdb_r": 0.14,
-                "absolute_percentile_clashscore": 0.0,
-                "absolute_percentile_percent_ramachandran_outliers": 12.8,
-                "absolute_percentile_percent_rotamer_outliers": 10.6,
-                "angles_rmsz": 7.11,
-                "attempted_validation_steps": "molprobity,validation-pack,mogul,buster-report,percentiles,writexml",
-                "bonds_rmsz": 9.69,
-                "clashscore": 141.11,
-                "high_resol_relative_percentile_clashscore": 1.72,
-                "high_resol_relative_percentile_percent_ramachandran_outliers": 1.72,
-                "high_resol_relative_percentile_percent_rotamer_outliers": 1.72,
-                "ligands_for_buster_report": "yes",
-                "low_resol_relative_percentile_clashscore": 1.76,
-                "low_resol_relative_percentile_percent_ramachandran_outliers": 1.76,
-                "low_resol_relative_percentile_percent_rotamer_outliers": 1.76,
-                "num_hreduce": 4456.0,
-                "num_pdbids_absolute_percentile_clashscore": 141614,
-                "num_pdbids_absolute_percentile_percent_ramachandran_outliers": 138981,
-                "num_pdbids_absolute_percentile_percent_rotamer_outliers": 138945,
-                "num_pdbids_relative_percentile_clashscore": 3923,
-                "num_pdbids_relative_percentile_percent_ramachandran_outliers": 3878,
-                "num_pdbids_relative_percentile_percent_rotamer_outliers": 3878,
-                "num_angles_rmsz": 6114,
-                "num_bonds_rmsz": 4500,
-                "percent_ramachandran_outliers": 1.24,
-                "percent_rotamer_outliers": 8.44,
-                "percentilebins": [
-                    "all",
-                    "1.74",
-                    "xray"
-                ],
-                "protein_dnarnaentities": "1,2",
-                "relative_percentile_clashscore": 0.0,
-                "relative_percentile_percent_ramachandran_outliers": 2.6,
-                "relative_percentile_percent_rotamer_outliers": 1.3,
-                "report_creation_date": "Mar  8, 2023 -- 01:17 AM EST",
-                "restypes_notchecked_for_bond_angle_geometry": [
-                    "PO4",
-                    "HEM"
-                ],
-                "pdbdeposition_date": "1984-03-07T00:00:00+0000",
-                "pdbresolution": 1.74,
-                "pdbrevision_date": "2023-03-15T00:00:00+0000",
-                "pdbrevision_number": 7.0
-            },
             "rcsb_accession_info": {
                 "deposit_date": "1984-03-07T00:00:00+0000",
                 "has_released_experimental_data": "N",

diff --git a/tests/test_enrichr.py b/tests/test_enrichr.py
@@ -14,7 +14,8 @@
     enrichr_dict = json.load(json_file)
 
 # Sleep time (in seconds) between tests to prevent surpassing the server rate limit
-sleep_time = 3
+
+sleep_time = 5
 
 class TestEnrichr(unittest.TestCase):
     def test_enrichr_pathway(self):