update khmer #49276
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,31 @@ | ||
| --- khmer-2.1.1/setup.py 2017-05-25 20:10:21.000000000 -0400 | ||
| +++ khmer-2.1.1/setup.py 2024-08-07 21:54:04.775775473 -0400 | ||
| @@ -123,8 +123,8 @@ | ||
| # change setup.cfg or use the `--libraries z,bz2` parameter which will make our | ||
| # custom build_ext command strip out the bundled versions. | ||
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| -ZLIBDIR = 'third-party/zlib' | ||
| -BZIP2DIR = 'third-party/bzip2' | ||
| +# ZLIBDIR = 'third-party/zlib' | ||
| +# BZIP2DIR = 'third-party/bzip2' | ||
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| BUILD_DEPENDS = [] | ||
| BUILD_DEPENDS.extend(path_join("lib", bn + ".hh") for bn in [ | ||
| @@ -259,7 +259,7 @@ | ||
| if sys.platform == 'darwin' and 'gcov' in self.libraries: | ||
| self.libraries.remove('gcov') | ||
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| - if "z" not in self.libraries: | ||
| + if False: | ||
| zcmd = ['bash', '-c', 'cd ' + ZLIBDIR + ' && ( test Makefile -nt' | ||
| ' configure || bash ./configure --static ) && make -f ' | ||
| 'Makefile.pic PIC'] | ||
| @@ -269,7 +269,7 @@ | ||
| "adler32", "compress", "crc32", "deflate", "gzclose", | ||
| "gzlib", "gzread", "gzwrite", "infback", "inffast", | ||
| "inflate", "inftrees", "trees", "uncompr", "zutil"]) | ||
| - if "bz2" not in self.libraries: | ||
| + if False: | ||
| bz2cmd = ['bash', '-c', 'cd ' + BZIP2DIR + ' && make -f ' | ||
| 'Makefile-libbz2_so all'] | ||
| spawn(cmd=bz2cmd, dry_run=self.dry_run) |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,13 @@ | ||
| --- khmer-2.1.1/setup.cfg 2017-05-25 20:10:21.000000000 -0400 | ||
| +++ khmer-2.1.1/setup.cfg 2024-08-07 22:04:20.100887810 -0400 | ||
| @@ -3,8 +3,8 @@ | ||
| undef = NO_UNIQUE_RC | ||
| # libraries = z,bz2 | ||
| ## if using system libraries | ||
| -include-dirs = lib:third-party/zlib:third-party/bzip2:third-party/seqan/core/include:third-party/smhasher | ||
| -# include-dirs = lib | ||
| +# include-dirs = lib:third-party/zlib:third-party/bzip2:third-party/seqan/core/include:third-party/smhasher | ||
| +include_dirs = lib:include:include/seqan:third-party/smhasher | ||
| ## if using system libraries (broken) | ||
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| # define = NDEBUG |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,21 @@ | ||
| --- khmer-2.1.1/MANIFEST.in | ||
| +++ khmer-2.1.1/MANIFEST.in | ||
| @@ -3,12 +3,12 @@ | ||
| include LICENSE TODO .ycm_extra_conf.py authors.csv | ||
| recursive-include lib *.hh *.cc [Mm]akefile* get_version.py | ||
| recursive-include khmer *.hh | ||
| -recursive-include third-party *.cc *.1 *.xsl README* sample* words* *.sh *.c | ||
| -recursive-include third-party manual* [Mm]akefile* *.pl *.dsp CHANGES *.txt *.h | ||
| -recursive-include third-party ChangeLog FAQ INDEX configure *.xsl | ||
| -recursive-include third-party/bzip2 bzip.css entities.xml libbz2.def LICENSE | ||
| -include third-party/zlib/zconf.h.in third-party/zlib/zlib.pc.in | ||
| -exclude third-party/zlib/Makefile third-party/zlib/zconf.h | ||
| +#recursive-include third-party *.cc *.1 *.xsl README* sample* words* *.sh *.c | ||
| +#recursive-include third-party manual* [Mm]akefile* *.pl *.dsp CHANGES *.txt *.h | ||
| +#recursive-include third-party ChangeLog FAQ INDEX configure *.xsl | ||
| +#recursive-include third-party/bzip2 bzip.css entities.xml libbz2.def LICENSE | ||
| +#include third-party/zlib/zconf.h.in third-party/zlib/zlib.pc.in | ||
| +#exclude third-party/zlib/Makefile third-party/zlib/zconf.h | ||
| recursive-include scripts README.txt | ||
| graft tests | ||
| include scripts/oxli |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,32 @@ | ||
| #!/bin/bash | ||
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| set -x -e | ||
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| # export variables for compiling | ||
| export INCLUDE_PATH="${BUILD_PREFIX}/include:${PWD}/third-party/seqan/core/include" | ||
| export LIBRARY_PATH="${BUILD_PREFIX}/lib" | ||
| export LD_LIBRARY_PATH="${LD_LIBRARY_PATH}:${PWD}/lib" | ||
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| export LDFLAGS="-L${BUILD_PREFIX}/lib -L${PWD}/third-party/seqan/core/include" | ||
| export CCPFLAGS="-I${BUILD_PREFIX}/include -I${PWD}/third-party/seqan/core/include" | ||
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| # create directories for compiling | ||
| mkdir -p $PREFIX/bin | ||
| mkdir -p $PREFIX/include | ||
| mkdir -p $PREFIX/lib | ||
| mkdir -p $PREFIX/scripts | ||
|
Comment on lines
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There was a problem hiding this comment. Add safety check for $PREFIX environment variable The script assumes $PREFIX is set but doesn't verify it. This could lead to unexpected behavior if the variable is unset. Add this check at the beginning of the script: set -x -e
+# Verify required environment variables
+if [ -z "${PREFIX}" ]; then
+ echo "Error: PREFIX environment variable is not set"
+ exit 1
+fi
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| # populate compiling directories | ||
| cp -v lib/* $PREFIX/include | ||
| cp -v scripts/* $PREFIX/bin | ||
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| # copies over third-party/seqan/core/include/seqan | ||
| mkdir -pv $PREFIX/include/seqan | ||
| cp -vr third-party/seqan/core/include/seqan/* $PREFIX/include/seqan/ | ||
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Comment on lines
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There was a problem hiding this comment. Fix incorrect file copying operations and add error handling There are several issues with the file copying operations:
Consider this improved implementation: -cp -v lib/* $PREFIX/include
-cp -v scripts/* $PREFIX/bin
+# Verify source directories exist
+for dir in lib scripts third-party/seqan/core/include/seqan; do
+ if [ ! -d "$dir" ]; then
+ echo "Error: Required directory $dir not found"
+ exit 1
+ fi
+done
+
+# Copy files to correct locations
+cp -v lib/* $PREFIX/lib || { echo "Error copying library files"; exit 1; }
+cp -v scripts/* $PREFIX/bin || { echo "Error copying scripts"; exit 1; }
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| # install khmer | ||
| $PYTHON -m pip install . --no-deps --no-build-isolation --no-cache-dir --use-pep517 -vvv | ||
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| # debugging line to find where khmer was installed | ||
| echo "here i am! ⊂◉‿◉つ " | ||
| ls -lhR | ||
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🛠️ Refactor suggestion
Review environment variable handling
The environment variable setup has several potential issues:
INCLUDE_PATHandLIBRARY_PATHcompletely override system paths instead of appendingthird-party/seqancould break if the directory structure changesLD_LIBRARY_PATHmight affect runtime behavior unexpectedlyConsider these improvements:
📝 Committable suggestion