Commit 9bc1f0c5 authored by Sean Solari's avatar Sean Solari
Browse files

Updated setup.py with extras_require

parent 12054b70
...@@ -8,7 +8,7 @@ then ...@@ -8,7 +8,7 @@ then
exit 1 exit 1
fi fi
rsync -vaRP docs src/expam test .gitignore .pyirc .readthedocs.yaml LICENSE MANIFEST.in pyproject.toml README.md setup.cfg setup.py buildandtwine.sh requirements.txt $EXPAM_PUBLIC_DIR rsync -vaRP docs src/expam src/benchmark test .gitignore .pyirc .readthedocs.yaml LICENSE MANIFEST.in pyproject.toml README.md setup.cfg setup.py buildandtwine.sh requirements.txt $EXPAM_PUBLIC_DIR
echo "\nbuildandtwine.sh" >> $EXPAM_PUBLIC_DIR/.gitignore echo "\nbuildandtwine.sh" >> $EXPAM_PUBLIC_DIR/.gitignore
echo "\n==================================\nLocal push completed successfully!\n==================================\n\nNow run build and run twine :)" echo "\n==================================\nLocal push completed successfully!\n==================================\n\nNow run build and run twine :)"
...@@ -109,16 +109,16 @@ setup( ...@@ -109,16 +109,16 @@ setup(
# #
python_requires=">=3.8", python_requires=">=3.8",
install_requires=[ install_requires=[
# "ete3",
# "PyQt5==5.12",
"numpy", "numpy",
"matplotlib", "matplotlib",
"pandas", "pandas",
"psutil", "psutil",
"requests", "requests",
# "sourmash",
"tables" "tables"
], ],
extras_require={
"treeplot": ["ete3", "PyQt5==5.12", "sourmash"]
},
# #
# Cython modules. # Cython modules.
# #
......
...@@ -107,7 +107,8 @@ class CleanRaw(Process): ...@@ -107,7 +107,8 @@ class CleanRaw(Process):
parts = line.strip().split('\t') parts = line.strip().split('\t')
try: try:
parts[2] = self.taxid_map[parts[2]] new_taxid = self.taxid_map[parts[2]]
parts[2] = new_taxid
except KeyError: except KeyError:
pass pass
...@@ -130,6 +131,8 @@ def make_results_compatible(db_path: str, results_config: ResultsPathConfig, bad ...@@ -130,6 +131,8 @@ def make_results_compatible(db_path: str, results_config: ResultsPathConfig, bad
taxid_map = find_compatible_names(db_path, bad_taxids) taxid_map = find_compatible_names(db_path, bad_taxids)
bad_taxids_set = set(bad_taxids) bad_taxids_set = set(bad_taxids)
print(taxid_map)
# Replace names in tax summary files. # Replace names in tax summary files.
summary_files = distribute(ls(results_config.tax, ext=".csv"), n) summary_files = distribute(ls(results_config.tax, ext=".csv"), n)
procs = [CleanSummary(summary_files[i], bad_taxids_set) for i in range(n)] procs = [CleanSummary(summary_files[i], bad_taxids_set) for i in range(n)]
......
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