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Issue 93 binder #99

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merged 4 commits into from
Jun 23, 2022
Merged

Issue 93 binder #99

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30f3fb9
Updated the seqrepo rest dp url, added files for binder environment i…
wesleygoar Jun 2, 2022
334ab63
refactor: change endpoint for vnorm rest dp, add tests, fix notebooks…
korikuzma Jun 3, 2022
4aba503
added --display-name="VRS_kernel" to help the user know which kernel …
wesleygoar Jun 6, 2022
55df168
Update python-cqa pytest command
korikuzma Jun 22, 2022
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6 changes: 6 additions & 0 deletions .binder/postBuild
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Original file line number Diff line number Diff line change
@@ -0,0 +1,6 @@
#!/bin/bash
set -e

make devready
source venv/3.9/bin/activate
python -m ipykernel install --user --name=3.9 --display-name="VRS_kernel"
1 change: 1 addition & 0 deletions .binder/requirements.txt
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@@ -0,0 +1 @@
jsonschema==3.2.0
1 change: 1 addition & 0 deletions .binder/runtime.txt
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@@ -0,0 +1 @@
python-3.9
2 changes: 1 addition & 1 deletion .github/workflows/python-cqa.yml
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Expand Up @@ -46,4 +46,4 @@ jobs:
pylint src/ga4gh/{core,vrs}
- name: Test with pytest
run: |
pytest
python -m pytest
1 change: 1 addition & 0 deletions .gitignore
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Expand Up @@ -19,3 +19,4 @@ notes
venv
.vscode/launch.json
lint
uta_*.pgd.gz
2 changes: 1 addition & 1 deletion notebooks/Associating Annotations.ipynb
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Expand Up @@ -24,7 +24,7 @@
"from ga4gh.vrs.extras.translator import Translator\n",
"\n",
"# Requires seqrepo REST interface is running on this URL (e.g., using docker image)\n",
"seqrepo_rest_service_url = \"http://localhost:5000/seqrepo/\"\n",
"seqrepo_rest_service_url = \"https://services.genomicmedlab.org/seqrepo\"\n",
"dp = SeqRepoRESTDataProxy(base_url=seqrepo_rest_service_url)\n",
"\n",
"tlr = Translator(data_proxy=dp)"
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17 changes: 10 additions & 7 deletions notebooks/Docs and Validation.ipynb
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Expand Up @@ -26,14 +26,14 @@
"Removing allOf attribute from AbsoluteCopyNumber to avoid python-jsonschema-objects error.\n",
"Removing allOf attribute from SequenceInterval to avoid python-jsonschema-objects error.\n",
"Removing allOf attribute from RepeatedSequenceExpression to avoid python-jsonschema-objects error.\n",
"/Users/kxk102/Documents/ga4gh/vrs/venv/lib/python3.9/site-packages/python_jsonschema_objects/__init__.py:49: UserWarning: Schema version http://json-schema.org/draft-07/schema not recognized. Some keywords and features may not be supported.\n",
"/Users/wag002/PycharmProjects/vrs-python/venv/3.9/lib/python3.9/site-packages/python_jsonschema_objects/__init__.py:49: UserWarning: Schema version http://json-schema.org/draft-07/schema not recognized. Some keywords and features may not be supported.\n",
" warnings.warn(\n"
]
},
{
"data": {
"text/plain": [
"'0.7.5.dev2+g781f8b6.d20220314'"
"'0.8a1.dev58+gf859a88.d20220601'"
]
},
"execution_count": 1,
Expand Down Expand Up @@ -476,7 +476,7 @@
"outputs": [],
"source": [
"from ga4gh.vrs.dataproxy import SeqRepoRESTDataProxy\n",
"seqrepo_rest_service_url = \"http://localhost:5000/seqrepo\"\n",
"seqrepo_rest_service_url = \"https://services.genomicmedlab.org/seqrepo\"\n",
"dp = SeqRepoRESTDataProxy(base_url=seqrepo_rest_service_url)"
]
},
Expand Down Expand Up @@ -546,7 +546,7 @@
{
"data": {
"text/plain": [
"['ga4gh:GS.IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl']"
"['ga4gh:SQ.IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl']"
]
},
"execution_count": 20,
Expand All @@ -566,7 +566,7 @@
{
"data": {
"text/plain": [
"['GRCh38:19', 'GRCh38:chr19']"
"['GRCh38:chr19', 'GRCh38:19']"
]
},
"execution_count": 21,
Expand Down Expand Up @@ -684,8 +684,11 @@
}
],
"metadata": {
"interpreter": {
"hash": "e3010397f827d762dd71da5e8c08c9d1e15db6c6cbe60e8a92c1e943686ce175"
},
"kernelspec": {
"display_name": "Python 3",
"display_name": "Python 3.9.11 ('3.9': venv)",
"language": "python",
"name": "python3"
},
Expand All @@ -699,7 +702,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.9.10"
"version": "3.9.11"
}
},
"nbformat": 4,
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