moose-classifier 1.0__tar.gz → 1.1__tar.gz

{moose_classifier-1.0 → moose_classifier-1.1}/.github/workflows/unittests.yml

@@ -13,14 +13,14 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-latest]
-        python-version: ['3.12', '3.11', '3.10', '3.9']
+        python-version: ['3.13', '3.12', '3.11', '3.10']
     steps:
     -
-      uses: actions/setup-python@v3
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
     -
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
     -
       name: Install and test
       run: |

{moose_classifier-1.0/src/moose_classifier.egg-info → moose_classifier-1.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: moose_classifier
-Version: 1.0
+Version: 1.1
 Summary: Alignment based taxonomic classifier
 Author: Chris Rosenthal
 Author-email: crosenth@gmail.com
@@ -18,6 +18,8 @@ Requires-Dist: pandas>=2.0.2
 
 # moose
 
+[![Unit Tests](https://github.com/crosenth/moose/actions/workflows/unittests.yml/badge.svg)](https://github.com/fhcrc/taxtastic/actions/workflows/unittests.yml) 
+
 A tool for taxonomically selecting, grouping and summarizing pairwise
 alignment classifications into something more concise and readable.
 

{moose_classifier-1.0 → moose_classifier-1.1}/README.md

@@ -1,5 +1,7 @@
 # moose
 
+[![Unit Tests](https://github.com/crosenth/moose/actions/workflows/unittests.yml/badge.svg)](https://github.com/fhcrc/taxtastic/actions/workflows/unittests.yml) 
+
 A tool for taxonomically selecting, grouping and summarizing pairwise
 alignment classifications into something more concise and readable.
 

{moose_classifier-1.0 → moose_classifier-1.1}/src/classify.py

@@ -220,10 +220,6 @@ def action(args):
         header = None
         sep = args.delimiter
         names = args.columns.split(',')
-    elif args.delimiter:
-        header = 0
-        sep = args.delimiter
-        names = None
     elif args.blast6:
         header = None
         sep = '\t'
@@ -236,7 +232,7 @@ def action(args):
         names = None
     else:
         header = 0
-        sep = ','
+        sep = args.delimiter
         names = None
 
     logging.info('loading alignments ' + str(args.alignments))
@@ -506,12 +502,12 @@ def action(args):
     qseqids['assignment'] = '[no blast result]'
     qseqids['assignment_hash'] = 0
     qseqids['assignment_tax_name'] = ''
-    qseqids['assignment_rank'] = ''
-    qseqids['assignment_rank'] = qseqids['assignment_rank'].astype(cat_ranks)
+    qseqids['assignment_rank'] = pd.Categorical(
+        [pd.NA] * len(qseqids), dtype=cat_ranks)
     qseqids['assignment_threshold'] = numpy.nan
     qseqids['condensed_id'] = ''
-    qseqids['condensed_rank'] = ''
-    qseqids['condensed_rank'] = qseqids['condensed_rank'].astype(cat_ranks)
+    qseqids['condensed_rank'] = pd.Categorical(
+        [pd.NA] * len(qseqids), dtype=cat_ranks)
     qseqids['starred'] = ''
 
     # add back qseqids that have no hits back into aligns

{moose_classifier-1.0 → moose_classifier-1.1/src/moose_classifier.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: moose_classifier
-Version: 1.0
+Version: 1.1
 Summary: Alignment based taxonomic classifier
 Author: Chris Rosenthal
 Author-email: crosenth@gmail.com
@@ -18,6 +18,8 @@ Requires-Dist: pandas>=2.0.2
 
 # moose
 
+[![Unit Tests](https://github.com/crosenth/moose/actions/workflows/unittests.yml/badge.svg)](https://github.com/fhcrc/taxtastic/actions/workflows/unittests.yml) 
+
 A tool for taxonomically selecting, grouping and summarizing pairwise
 alignment classifications into something more concise and readable.
 

{moose_classifier-1.0 → moose_classifier-1.1}/src/moose_classifier.egg-info/SOURCES.txt

@@ -18,6 +18,8 @@ src/moose_classifier.egg-info/SOURCES.txt
 src/moose_classifier.egg-info/dependency_links.txt
 src/moose_classifier.egg-info/entry_points.txt
 src/moose_classifier.egg-info/requires.txt
+src/moose_classifier.egg-info/scm_file_list.json
+src/moose_classifier.egg-info/scm_version.json
 src/moose_classifier.egg-info/top_level.txt
 testfiles/rank_thresholds.csv
 testfiles/rrnDB_16S_copy_num.csv.bz2

moose_classifier-1.1/src/moose_classifier.egg-info/scm_file_list.json

@@ -0,0 +1,76 @@
+{
+  "files": [
+    ".github/workflows/publish-pypi.yml",
+    ".github/workflows/unittests.yml",
+    ".gitignore",
+    "README.md",
+    "pyproject.toml",
+    "requirements.txt",
+    "sphinx/Makefile",
+    "sphinx/classifier.rst",
+    "sphinx/conf.py",
+    "sphinx/index.rst",
+    "sphinx/make.bat",
+    "sphinx/modules.rst",
+    "src/classify.py",
+    "src/lineages.py",
+    "src/version.py",
+    "testfiles/TestClassify/blast.csv.bz2",
+    "testfiles/TestClassify/blast_3strepto.csv",
+    "testfiles/TestClassify/blast_extrafields.csv.bz2",
+    "testfiles/TestClassify/map.csv.bz2",
+    "testfiles/TestClassify/map_single.csv.bz2",
+    "testfiles/TestClassify/seq_info.csv.bz2",
+    "testfiles/TestClassify/taxonomy.csv.bz2",
+    "testfiles/TestClassify/test01/classifications.csv.bz2",
+    "testfiles/TestClassify/test01/details.csv.bz2",
+    "testfiles/TestClassify/test02/classifications.csv.bz2",
+    "testfiles/TestClassify/test02/details.csv.bz2",
+    "testfiles/TestClassify/test02/map_single.csv.bz2",
+    "testfiles/TestClassify/test03/classifications.csv.bz2",
+    "testfiles/TestClassify/test03/details.csv.bz2",
+    "testfiles/TestClassify/test06/classifications.csv.bz2",
+    "testfiles/TestClassify/test06/details.csv.bz2",
+    "testfiles/TestClassify/test06/map.csv.bz2",
+    "testfiles/TestClassify/test07/blast.csv.bz2",
+    "testfiles/TestClassify/test07/classifications.csv.bz2",
+    "testfiles/TestClassify/test07/details.csv.bz2",
+    "testfiles/TestClassify/test07/map.csv.bz2",
+    "testfiles/TestClassify/test07/seq_info.csv.bz2",
+    "testfiles/TestClassify/test07/taxonomy.csv.bz2",
+    "testfiles/TestClassify/test08/classifications.csv.bz2",
+    "testfiles/TestClassify/test08/details.csv.bz2",
+    "testfiles/TestClassify/test09/blast.csv.bz2",
+    "testfiles/TestClassify/test09/classifications.csv.bz2",
+    "testfiles/TestClassify/test09/details.csv.bz2",
+    "testfiles/TestClassify/test09/map.csv.bz2",
+    "testfiles/TestClassify/test10/classifications.csv.bz2",
+    "testfiles/TestClassify/test10/details.csv.bz2",
+    "testfiles/TestClassify/test11/blast.csv.bz2",
+    "testfiles/TestClassify/test11/classifications.csv.bz2",
+    "testfiles/TestClassify/test11/details.csv.bz2",
+    "testfiles/TestClassify/test11/seq_info.csv.bz2",
+    "testfiles/TestClassify/test11/taxonomy.csv.bz2",
+    "testfiles/TestClassify/test12/map_single.csv.bz2",
+    "testfiles/TestClassify/test13/blast.csv.bz2",
+    "testfiles/TestClassify/test13/classifications.csv.bz2",
+    "testfiles/TestClassify/test13/seq_info.csv.bz2",
+    "testfiles/TestClassify/test13/weights.csv.bz2",
+    "testfiles/TestClassify/test14/classifications.csv.bz2",
+    "testfiles/TestClassify/test14/details.csv.bz2",
+    "testfiles/TestClassify/test15/classifications.csv.bz2",
+    "testfiles/TestClassify/test15/details.csv.bz2",
+    "testfiles/TestClassify/test16/classifications.csv.bz2",
+    "testfiles/TestClassify/test16/details.csv.bz2",
+    "testfiles/TestClassify/test17/classifications.csv.bz2",
+    "testfiles/TestClassify/test17/details.csv.bz2",
+    "testfiles/TestClassify/test18/classifications.csv.bz2",
+    "testfiles/TestClassify/test18/details.csv.bz2",
+    "testfiles/TestClassify/weights.csv.bz2",
+    "testfiles/rank_thresholds.csv",
+    "testfiles/rrnDB_16S_copy_num.csv.bz2",
+    "testfiles/taxonomy.csv.bz2",
+    "tests/__init__.py",
+    "tests/test_classify.py"
+  ]
+}

moose_classifier-1.1/src/moose_classifier.egg-info/scm_version.json

@@ -0,0 +1,8 @@
+{
+  "tag": "1.1",
+  "distance": 0,
+  "node": "g51a0c0d9324b51eaecbf403faf35f0a70c504221",
+  "dirty": false,
+  "branch": "HEAD",
+  "node_date": "2026-10-02"
+}