[med-svn] [Git][med-team/xpore][master] 4 commits: Added gbp.conf

[Israel Komolehin (@Komolehin)]

Israel Komolehin pushed to branch master at Debian Med / xpore


Commits:
cd902407 by Komolehin Israel Timilehin at 2023-12-28T05:46:41+00:00
Added gbp.conf

- - - - -
f5be4ecc by Komolehin Israel Timilehin at 2023-12-28T05:47:35+00:00
New upstream version 2.1
- - - - -
b8eb19b0 by Komolehin Israel Timilehin at 2023-12-28T05:48:48+00:00
Update upstream source from tag 'upstream/2.1'

Update to upstream version '2.1'
with Debian dir 6383e5db2bae2b87f95509de56693214f484cf21
- - - - -
817aae64 by Komolehin Israel Timilehin at 2023-12-28T18:25:40+00:00
Added Autopkgtest

- - - - -


6 changed files:

- − .gitattributes
- − .gitignore
- + debian-tests-data/demo.tar.gz
- + debian/gbp.conf
- + debian/tests/control
- + debian/tests/run-data-preprocess-test


Changes:

=====================================
.gitattributes deleted
=====================================
@@ -1,2 +0,0 @@
-db/** filter=lfs diff=lfs merge=lfs -text
-tests/** filter=lfs diff=lfs merge=lfs -text


=====================================
.gitignore deleted
=====================================
@@ -1,136 +0,0 @@
-# Large files
-#tests/
-#db/
-
-# Byte-compiled / optimized / DLL files
-__pycache__/
-*.py[cod]
-*$py.class
-
-# C extensions
-*.so
-
-# Distribution / packaging
-.Python
-build/
-develop-eggs/
-dist/
-downloads/
-eggs/
-.eggs/
-lib/
-lib64/
-parts/
-sdist/
-var/
-wheels/
-pip-wheel-metadata/
-share/python-wheels/
-*.egg-info/
-.installed.cfg
-*.egg
-MANIFEST
-
-# PyInstaller
-#  Usually these files are written by a python script from a template
-#  before PyInstaller builds the exe, so as to inject date/other infos into it.
-*.manifest
-*.spec
-
-# Installer logs
-pip-log.txt
-pip-delete-this-directory.txt
-
-# Unit test / coverage reports
-htmlcov/
-.tox/
-.nox/
-.coverage
-.coverage.*
-.cache
-nosetests.xml
-coverage.xml
-*.cover
-*.py,cover
-.hypothesis/
-.pytest_cache/
-
-# Translations
-*.mo
-*.pot
-
-# Django stuff:
-*.log
-local_settings.py
-db.sqlite3
-db.sqlite3-journal
-
-# Flask stuff:
-instance/
-.webassets-cache
-
-# Scrapy stuff:
-.scrapy
-
-# Sphinx documentation
-docs/_build/
-
-# PyBuilder
-target/
-
-# Jupyter Notebook
-.ipynb_checkpoints
-
-# IPython
-profile_default/
-ipython_config.py
-
-# pyenv
-.python-version
-
-# pipenv
-#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
-#   However, in case of collaboration, if having platform-specific dependencies or dependencies
-#   having no cross-platform support, pipenv may install dependencies that don't work, or not
-#   install all needed dependencies.
-#Pipfile.lock
-
-# PEP 582; used by e.g. github.com/David-OConnor/pyflow
-__pypackages__/
-
-# Celery stuff
-celerybeat-schedule
-celerybeat.pid
-
-# SageMath parsed files
-*.sage.py
-
-# Environments
-.env
-.venv
-env/
-venv/
-ENV/
-env.bak/
-venv.bak/
-
-# Spyder project settings
-.spyderproject
-.spyproject
-
-# Rope project settings
-.ropeproject
-
-# mkdocs documentation
-/site
-
-# mypy
-.mypy_cache/
-.dmypy.json
-dmypy.json
-
-# Pyre type checker
-.pyre/
-
-# DS store
-.DS_Store


=====================================
debian-tests-data/demo.tar.gz
=====================================
Binary files /dev/null and b/debian-tests-data/demo.tar.gz differ


=====================================
debian/gbp.conf
=====================================
@@ -0,0 +1,4 @@
+[DEFAULT]
+pristine-tar=True
+filter=[ '.gitignore', '.travis.yml', '.git*' ]
+component=[ 'debian-tests-data' ]
\ No newline at end of file


=====================================
debian/tests/control
=====================================
@@ -0,0 +1,3 @@
+Tests: run-data-preprocess-test
+Depends: xpore
+Restrictions: allow-stderr


=====================================
debian/tests/run-data-preprocess-test
=====================================
@@ -0,0 +1,40 @@
+#!/bin/bash
+
+CUR_DIR=`pwd`
+
+if [ "$AUTOPKGTEST_TMP" = "" ]; then
+	AUTOPKGTEST_TMP=`mktemp -d /tmp/${pkg}-test.XXXX`
+
+	trap "rm -rf $AUTOPKG_TMP" 0 INT QUIT ABRT PIPE TERM
+
+fi
+
+mkdir -p "$AUTOPKGTEST_TMP"/tests
+
+# Copy test dataset
+cp -a "${CUR_DIR}"/debian-tests-data/* "$AUTOPKGTEST_TMP"/tests
+
+
+cd "$AUTOPKGTEST_TMP"/tests/
+
+# Extract demo dataset
+tar -xvf demo.tar.gz
+
+# Change directory to a dataset dir
+cd demo/data/HEK293T-METTL3-KO-rep1/
+
+# Run within the dataset dir
+xpore dataprep --eventalign nanopolish/eventalign.txt --gtf_or_gff ../../demo.gtf --transcript_fasta ../../demo.fa --out_dir dataprep --genome
+
+# Check output directory
+if [ -d "./dataprep" ]; then
+
+    echo "Output Directory Generated"
+    echo "PASS"
+
+else
+
+    echo "Output Directory Not Generated"
+    exit 1
+
+fi



View it on GitLab: https://salsa.debian.org/med-team/xpore/-/compare/bea8751ee62ee65ba9720fbfce3f73d3ea59108c...817aae649690b94ff581134d9b401c0f8794c71e

-- 
View it on GitLab: https://salsa.debian.org/med-team/xpore/-/compare/bea8751ee62ee65ba9720fbfce3f73d3ea59108c...817aae649690b94ff581134d9b401c0f8794c71e
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