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commit b3e49cd60d2a43496b354d1d0210b6262ebcbf44 Author: Afif Elghraoui <[email protected]> Date: Mon Oct 26 21:53:00 2015 -0700 Drop rename-dataset.py patch in favor of build-time substitution Maintaining the patch is unwieldy. Making the substitution at build time using sed should be more robust. --- debian/patches/rename-datasetpy.patch | 179 ---------------------------------- debian/patches/series | 1 - debian/rules | 1 + 3 files changed, 1 insertion(+), 180 deletions(-) diff --git a/debian/patches/rename-datasetpy.patch b/debian/patches/rename-datasetpy.patch deleted file mode 100644 index 04e1ebe..0000000 --- a/debian/patches/rename-datasetpy.patch +++ /dev/null @@ -1,179 +0,0 @@ -Description: Rename dataset.py to pbdataset - dataset.py is not a name suitable for system-wide installation. It - is referenced by several parts of the source distribution here (especially - the tests), so this patch corrects those references. Upstream is not interested - in renaming since system-wide installation was not their intention for - this package [1]. -Author: Afif Elghraoui -Forwarded: https://github.com/PacificBiosciences/pbcore/issues/21#issuecomment-141742545 -Last-Update: 2015-09-20 ---- python-pbcore.orig/tests/test_pbdataset.py -+++ python-pbcore/tests/test_pbdataset.py -@@ -22,7 +22,7 @@ - - log = logging.getLogger(__name__) - --datasetpy_not_available = subprocess.call(["which", "dataset.py"]) -+datasetpy_not_available = subprocess.call(["which", "pbdataset"]) - - class TestDataSet(unittest.TestCase): - """Unit and integrationt tests for the DataSet class and \ -@@ -86,7 +86,7 @@ - "pbdataset script is not available") - def test_split_cli(self): - outdir = tempfile.mkdtemp(suffix="dataset-unittest") -- cmd = "dataset.py split --outdir {o} --contigs --chunks 2 {d}".format( -+ cmd = "pbdataset split --outdir {o} --contigs --chunks 2 {d}".format( - o=outdir, - d=data.getXml(8)) - log.debug(cmd) -@@ -102,7 +102,7 @@ - def test_create_cli(self): - log.debug("Absolute") - outdir = tempfile.mkdtemp(suffix="dataset-unittest") -- cmd = "dataset.py create --type AlignmentSet {o} {i1} {i2}".format( -+ cmd = "pbdataset create --type AlignmentSet {o} {i1} {i2}".format( - o=os.path.join(outdir, 'pbalchemysim.alignmentset.xml'), - i1=data.getXml(8), i2=data.getXml(11)) - log.debug(cmd) -@@ -113,7 +113,7 @@ - - log.debug("Relative") - outdir = tempfile.mkdtemp(suffix="dataset-unittest") -- cmd = ("dataset.py create --relative --type AlignmentSet " -+ cmd = ("pbdataset create --relative --type AlignmentSet " - "{o} {i1} {i2}".format( - o=os.path.join(outdir, 'pbalchemysim.alignmentset.xml'), - i1=data.getXml(8), ---- python-pbcore.orig/tests/test_pbdataset_subtypes.py -+++ python-pbcore/tests/test_pbdataset_subtypes.py -@@ -270,7 +270,7 @@ - outdir = tempfile.mkdtemp(suffix="dataset-unittest") - datafile = os.path.join(outdir, "merged.bam") - xmlfile = os.path.join(outdir, "merged.xml") -- cmd = "dataset.py consolidate {i} {d} {x}".format(i=data.getXml(12), -+ cmd = "pbdataset consolidate {i} {d} {x}".format(i=data.getXml(12), - d=datafile, - x=xmlfile) - log.debug(cmd) -@@ -304,7 +304,7 @@ - outdir = tempfile.mkdtemp(suffix="dataset-unittest") - datafile = os.path.join(outdir, "merged.bam") - xmlfile = os.path.join(outdir, "merged.xml") -- cmd = "dataset.py consolidate --numFiles 2 {i} {d} {x}".format( -+ cmd = "pbdataset consolidate --numFiles 2 {i} {d} {x}".format( - i=testFile, d=datafile, x=xmlfile) - log.debug(cmd) - o, r, m = backticks(cmd) ---- python-pbcore.orig/doc/pbcore.io.dataset.rst -+++ python-pbcore/doc/pbcore.io.dataset.rst -@@ -9,20 +9,20 @@ - The API and console entry points are designed with the set operations one might - perform on the various types of data held by a DataSet XML in mind: merge, - split, write etc. While various types of DataSets can be found in XML files, --the API (and in a way the console entry point, dataset.py) has DataSet as its -+the API (and in a way the console entry point, pbdataset) has DataSet as its - base type, with various subtypes extending or replacing functionality as - needed. - - - Console Entry Point Usage - ============================= --The following entry points are available through the main script: dataset.py:: -+The following entry points are available through the main script: pbdataset:: - -- usage: dataset.py [-h] [-v] [--debug] -+ usage: pbdataset [-h] [-v] [--debug] - {create,filter,merge,split,validate,loadstats,consolidate} - ... - -- Run dataset.py by specifying a command. -+ Run pbdataset by specifying a command. - - optional arguments: - -h, --help show this help message and exit -@@ -35,7 +35,7 @@ - - Create:: - -- usage: dataset.py create [-h] [--type DSTYPE] [--novalidate] [--relative] -+ usage: pbdataset create [-h] [--type DSTYPE] [--novalidate] [--relative] - outfile infile [infile ...] - - Create an XML file from a fofn or bam -@@ -53,7 +53,7 @@ - - Filter:: - -- usage: dataset.py filter [-h] infile outfile filters [filters ...] -+ usage: pbdataset filter [-h] infile outfile filters [filters ...] - - Add filters to an XML file - -@@ -67,7 +67,7 @@ - - Union:: - -- usage: dataset.py union [-h] outfile infiles [infiles ...] -+ usage: pbdataset union [-h] outfile infiles [infiles ...] - - Combine XML (and BAM) files - -@@ -80,7 +80,7 @@ - - Validate:: - -- usage: dataset.py validate [-h] infile -+ usage: pbdataset validate [-h] infile - - Validate ResourceId files (XML validation only available in testing) - -@@ -92,7 +92,7 @@ - - Load PipeStats:: - -- usage: dataset.py loadstats [-h] [--outfile OUTFILE] infile statsfile -+ usage: pbdataset loadstats [-h] [--outfile OUTFILE] infile statsfile - - Load an sts.xml file into a DataSet XML file - -@@ -106,7 +106,7 @@ - - Split:: - -- usage: dataset.py split [-h] [--contigs] [--chunks CHUNKS] [--subdatasets] -+ usage: pbdataset split [-h] [--contigs] [--chunks CHUNKS] [--subdatasets] - [--outdir OUTDIR] - infile ... - -@@ -145,8 +145,8 @@ - - 2. Merge the files into a FOFN-like dataset (bams aren't touched):: - -- # dataset.py merge <out_fn> <in_fn> [<in_fn> <in_fn> ...] -- dataset.py merge merged.alignmentset.xml movie1.alignmentset.xml movie2.alignmentset.xml -+ # pbdataset merge <out_fn> <in_fn> [<in_fn> <in_fn> ...] -+ pbdataset merge merged.alignmentset.xml movie1.alignmentset.xml movie2.alignmentset.xml - - 3. Split the dataset into chunks by contig (rname) (bams aren't touched). Note - that supplying output files splits the dataset into that many output files -@@ -155,7 +155,7 @@ - automatically. Specifying a number of chunks instead will produce that many - files, with contig or even sub contig (reference window) splitting.:: - -- dataset.py split --contigs --chunks 8 merged.alignmentset.xml -+ pbdataset split --contigs --chunks 8 merged.alignmentset.xml - - 4. Quiver then consumes these chunks:: - ---- python-pbcore.orig/bin/dataset.py -+++ python-pbcore/bin/dataset.py -@@ -38,7 +38,7 @@ - return parser - - def get_parser(): -- description = 'Run dataset.py by specifying a command.' -+ description = 'Run pbdataset by specifying a command.' - parser = argparse.ArgumentParser(version=__VERSION__, - description=description) - parser.add_argument("--debug", default=False, action='store_true', diff --git a/debian/patches/series b/debian/patches/series index 8944739..57f5ddc 100644 --- a/debian/patches/series +++ b/debian/patches/series @@ -1,3 +1,2 @@ doc-theme.patch enable-build-time-testing.patch -rename-datasetpy.patch diff --git a/debian/rules b/debian/rules index a8eec36..f867f98 100755 --- a/debian/rules +++ b/debian/rules @@ -19,6 +19,7 @@ override_dh_auto_build: override_dh_install: dh_install + find $(DESTDIR) -type f -exec sed -i 's/dataset\.py/pbdataset/g' {} + mv $(DESTDIR)/usr/bin/.open $(DESTDIR)/usr/bin/pbopen mv $(DESTDIR)/usr/bin/dataset.py $(DESTDIR)/usr/bin/pbdataset -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/python-pbcore.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
