diff --git a/README.md b/README.md index 048d5c0c..da07d7a3 100644 --- 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 index 940ec3d4..a6daa5eb 100644 --- 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 index 7f786f67..06693404 100644 --- 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 index bd1d1e1f..f2655a19 100644 --- 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 index 744e336a..b3c17f94 100644 --- 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):