Cogent3 License — cogent3 2024.11.09 documentation

{"diffoscope-json-version": 1, "source1": "/srv/reproducible-results/rbuild-debian/r-b-build.9V06TGWp/b1/python-cogent_2024.5.7a1+dfsg-3_amd64.changes", "source2": "/srv/reproducible-results/rbuild-debian/r-b-build.9V06TGWp/b2/python-cogent_2024.5.7a1+dfsg-3_amd64.changes", "unified_diff": null, "details": [{"source1": "Files", "source2": "Files", "unified_diff": "@@ -1,3 +1,3 @@\n \n- aa53518d9b57296d50942d38d2a3a7e2 16080920 doc optional python-cogent-doc_2024.5.7a1+dfsg-3_all.deb\n+ 78a999669ed6577a0c22c524e2aa991c 16081204 doc optional python-cogent-doc_2024.5.7a1+dfsg-3_all.deb\n b0fce8ce7e973d3b59abb51d2481546d 2001828 python optional python3-cogent3_2024.5.7a1+dfsg-3_amd64.deb\n"}, {"source1": "python-cogent-doc_2024.5.7a1+dfsg-3_all.deb", "source2": "python-cogent-doc_2024.5.7a1+dfsg-3_all.deb", "unified_diff": null, "details": [{"source1": "file list", "source2": "file list", "unified_diff": "@@ -1,3 +1,3 @@\n -rw-r--r-- 0 0 0 4 2024-07-05 16:45:00.000000 debian-binary\n--rw-r--r-- 0 0 0 11860 2024-07-05 16:45:00.000000 control.tar.xz\n--rw-r--r-- 0 0 0 16068868 2024-07-05 16:45:00.000000 data.tar.xz\n+-rw-r--r-- 0 0 0 11872 2024-07-05 16:45:00.000000 control.tar.xz\n+-rw-r--r-- 0 0 0 16069140 2024-07-05 16:45:00.000000 data.tar.xz\n"}, {"source1": "control.tar.xz", "source2": "control.tar.xz", "unified_diff": null, "details": [{"source1": "control.tar", "source2": "control.tar", "unified_diff": null, "details": [{"source1": "./md5sums", "source2": "./md5sums", "unified_diff": null, "details": [{"source1": "./md5sums", "source2": "./md5sums", "comments": ["Files differ"], "unified_diff": null}]}]}]}, {"source1": "data.tar.xz", "source2": "data.tar.xz", "unified_diff": null, "details": [{"source1": "data.tar", "source2": "data.tar", "unified_diff": null, "details": [{"source1": "./usr/share/doc/python-cogent-doc/html/COGENT3_LICENSE.html", "source2": "./usr/share/doc/python-cogent-doc/html/COGENT3_LICENSE.html", "unified_diff": "@@ -4,26 +4,26 @@\n \n \n \n \n \n \n \n- Cogent3 License — cogent3 2024.11.09 documentation\n+ Cogent3 License — cogent3 2025.12.14 documentation\n \n \n \n \n \n \n \n- \n+ \n \n \n \n \n \n \n \n"}, {"source1": "./usr/share/doc/python-cogent-doc/html/_static/documentation_options.js", "source2": "./usr/share/doc/python-cogent-doc/html/_static/documentation_options.js", "unified_diff": null, "details": [{"source1": "js-beautify {}", "source2": "js-beautify {}", "unified_diff": "@@ -1,9 +1,9 @@\n const DOCUMENTATION_OPTIONS = {\n- VERSION: '2024.11.09',\n+ VERSION: '2025.12.14',\n LANGUAGE: 'en',\n COLLAPSE_INDEX: false,\n BUILDER: 'html',\n FILE_SUFFIX: '.html',\n LINK_SUFFIX: '.html',\n HAS_SOURCE: true,\n SOURCELINK_SUFFIX: '.txt',\n"}]}, {"source1": "./usr/share/doc/python-cogent-doc/html/api/__init__/cogent3.__init__.available_apps.html", "source2": "./usr/share/doc/python-cogent-doc/html/api/__init__/cogent3.__init__.available_apps.html", "unified_diff": "@@ -4,26 +4,26 @@\n \n \n \n \n \n \n \n- available_apps — cogent3 2024.11.09 documentation\n+ available_apps — cogent3 2025.12.14 documentation\n \n \n \n \n \n \n \n- \n+ \n \n \n \n \n \n \n \n"}, {"source1": "./usr/share/doc/python-cogent-doc/html/api/__init__/cogent3.__init__.available_codes.html", "source2": "./usr/share/doc/python-cogent-doc/html/api/__init__/cogent3.__init__.available_codes.html", "unified_diff": "@@ -4,26 +4,26 @@\n \n \n \n \n \n \n \n- available_codes — cogent3 2024.11.09 documentation\n+ available_codes — cogent3 2025.12.14 documentation\n \n \n \n \n \n \n \n- \n+ \n \n \n \n \n \n \n \n"}, {"source1": "./usr/share/doc/python-cogent-doc/html/api/__init__/cogent3.__init__.available_models.html", "source2": "./usr/share/doc/python-cogent-doc/html/api/__init__/cogent3.__init__.available_models.html", "unified_diff": "@@ -4,26 +4,26 @@\n \n \n \n \n \n \n \n- available_models — cogent3 2024.11.09 documentation\n+ available_models — cogent3 2025.12.14 documentation\n \n \n \n \n \n \n \n- \n+ \n \n \n \n \n \n \n \n"}, {"source1": "./usr/share/doc/python-cogent-doc/html/api/__init__/cogent3.__init__.available_moltypes.html", "source2": "./usr/share/doc/python-cogent-doc/html/api/__init__/cogent3.__init__.available_moltypes.html", "unified_diff": "@@ -4,26 +4,26 @@\n \n \n \n \n \n \n \n- available_moltypes — cogent3 2024.11.09 documentation\n+ available_moltypes — cogent3 2025.12.14 documentation\n \n \n \n \n \n \n \n- \n+ \n \n \n \n \n \n \n \n"}, {"source1": "./usr/share/doc/python-cogent-doc/html/api/__init__/cogent3.__init__.get_code.html", "source2": "./usr/share/doc/python-cogent-doc/html/api/__init__/cogent3.__init__.get_code.html", "unified_diff": "@@ -4,26 +4,26 @@\n \n \n \n \n \n \n \n- get_code — cogent3 2024.11.09 documentation\n+ get_code — cogent3 2025.12.14 documentation\n \n \n \n \n \n \n \n- \n+ \n \n \n \n \n \n \n \n"}, {"source1": "./usr/share/doc/python-cogent-doc/html/api/__init__/cogent3.__init__.get_model.html", "source2": "./usr/share/doc/python-cogent-doc/html/api/__init__/cogent3.__init__.get_model.html", "unified_diff": "@@ -4,26 +4,26 @@\n \n \n \n \n \n \n \n- get_model — cogent3 2024.11.09 documentation\n+ get_model — cogent3 2025.12.14 documentation\n \n \n \n \n \n \n \n- \n+ \n \n \n \n \n \n \n \n"}, {"source1": "./usr/share/doc/python-cogent-doc/html/api/__init__/cogent3.__init__.get_moltype.html", "source2": "./usr/share/doc/python-cogent-doc/html/api/__init__/cogent3.__init__.get_moltype.html", "unified_diff": "@@ -4,26 +4,26 @@\n \n \n \n \n \n \n \n- get_moltype — cogent3 2024.11.09 documentation\n+ get_moltype — cogent3 2025.12.14 documentation\n \n \n \n \n \n \n \n- \n+ \n \n \n \n \n \n \n \n"}, {"source1": "./usr/share/doc/python-cogent-doc/html/api/__init__/cogent3.__init__.load_aligned_seqs.html", "source2": "./usr/share/doc/python-cogent-doc/html/api/__init__/cogent3.__init__.load_aligned_seqs.html", "unified_diff": "@@ -4,26 +4,26 @@\n \n \n \n \n \n \n \n- load_aligned_seqs — cogent3 2024.11.09 documentation\n+ load_aligned_seqs — cogent3 2025.12.14 documentation\n \n \n \n \n \n \n \n- \n+ \n \n \n \n \n \n \n \n"}, {"source1": "./usr/share/doc/python-cogent-doc/html/api/__init__/cogent3.__init__.load_annotations.html", "source2": "./usr/share/doc/python-cogent-doc/html/api/__init__/cogent3.__init__.load_annotations.html", "unified_diff": "@@ -4,26 +4,26 @@\n \n \n \n \n \n \n \n- load_annotations — cogent3 2024.11.09 documentation\n+ load_annotations — cogent3 2025.12.14 documentation\n \n \n \n \n \n \n \n- \n+ \n \n \n \n \n \n \n \n"}, {"source1": "./usr/share/doc/python-cogent-doc/html/api/__init__/cogent3.__init__.load_delimited.html", "source2": "./usr/share/doc/python-cogent-doc/html/api/__init__/cogent3.__init__.load_delimited.html", "unified_diff": "@@ -4,26 +4,26 @@\n \n \n \n \n \n \n \n- load_delimited — cogent3 2024.11.09 documentation\n+ load_delimited — cogent3 2025.12.14 documentation\n \n \n \n \n \n \n \n- \n+ \n \n \n \n \n \n \n \n"}, {"source1": "./usr/share/doc/python-cogent-doc/html/api/__init__/cogent3.__init__.load_seq.html", "source2": "./usr/share/doc/python-cogent-doc/html/api/__init__/cogent3.__init__.load_seq.html", "unified_diff": "@@ -4,26 +4,26 @@\n \n \n \n \n \n \n \n- load_seq — cogent3 2024.11.09 documentation\n+ load_seq — cogent3 2025.12.14 documentation\n \n \n \n \n \n \n \n- \n+ \n \n \n \n \n \n \n \n"}, {"source1": "./usr/share/doc/python-cogent-doc/html/api/__init__/cogent3.__init__.load_table.html", "source2": "./usr/share/doc/python-cogent-doc/html/api/__init__/cogent3.__init__.load_table.html", "unified_diff": "@@ -4,26 +4,26 @@\n \n \n \n \n \n \n \n- load_table — cogent3 2024.11.09 documentation\n+ load_table — cogent3 2025.12.14 documentation\n \n \n \n \n \n \n \n- \n+ \n \n \n \n \n \n \n \n"}, {"source1": "./usr/share/doc/python-cogent-doc/html/api/__init__/cogent3.__init__.load_tree.html", "source2": "./usr/share/doc/python-cogent-doc/html/api/__init__/cogent3.__init__.load_tree.html", "unified_diff": "@@ -4,26 +4,26 @@\n \n \n \n \n \n \n \n- load_tree — cogent3 2024.11.09 documentation\n+ load_tree — cogent3 2025.12.14 documentation\n \n \n \n \n \n \n \n- \n+ \n \n \n \n \n \n \n \n"}, {"source1": "./usr/share/doc/python-cogent-doc/html/api/__init__/cogent3.__init__.load_unaligned_seqs.html", "source2": "./usr/share/doc/python-cogent-doc/html/api/__init__/cogent3.__init__.load_unaligned_seqs.html", "unified_diff": "@@ -4,26 +4,26 @@\n \n \n \n \n \n \n \n- load_unaligned_seqs — cogent3 2024.11.09 documentation\n+ load_unaligned_seqs — cogent3 2025.12.14 documentation\n \n \n \n \n \n \n \n- \n+ \n \n \n \n \n \n \n \n"}, {"source1": "./usr/share/doc/python-cogent-doc/html/api/__init__/cogent3.__init__.make_aligned_seqs.html", "source2": "./usr/share/doc/python-cogent-doc/html/api/__init__/cogent3.__init__.make_aligned_seqs.html", "unified_diff": "@@ -4,26 +4,26 @@\n \n \n \n \n \n \n \n- make_aligned_seqs — cogent3 2024.11.09 documentation\n+ make_aligned_seqs — cogent3 2025.12.14 documentation\n \n \n \n \n \n \n \n- \n+ \n \n \n \n \n \n \n \n"}, {"source1": "./usr/share/doc/python-cogent-doc/html/api/__init__/cogent3.__init__.make_seq.html", "source2": "./usr/share/doc/python-cogent-doc/html/api/__init__/cogent3.__init__.make_seq.html", "unified_diff": "@@ -4,26 +4,26 @@\n \n \n \n \n \n \n \n- make_seq — cogent3 2024.11.09 documentation\n+ make_seq — cogent3 2025.12.14 documentation\n \n \n \n \n \n \n \n- \n+ \n \n \n \n \n \n \n \n"}, {"source1": "./usr/share/doc/python-cogent-doc/html/api/__init__/cogent3.__init__.make_table.html", "source2": "./usr/share/doc/python-cogent-doc/html/api/__init__/cogent3.__init__.make_table.html", "unified_diff": "@@ -4,26 +4,26 @@\n \n \n \n \n \n \n \n- make_table — cogent3 2024.11.09 documentation\n+ make_table — cogent3 2025.12.14 documentation\n \n \n \n \n \n \n \n- \n+ \n \n \n \n \n \n \n \n"}, {"source1": "./usr/share/doc/python-cogent-doc/html/api/__init__/cogent3.__init__.make_tree.html", "source2": "./usr/share/doc/python-cogent-doc/html/api/__init__/cogent3.__init__.make_tree.html", "unified_diff": "@@ -4,26 +4,26 @@\n \n \n \n \n \n \n \n- make_tree — cogent3 2024.11.09 documentation\n+ make_tree — cogent3 2025.12.14 documentation\n \n \n \n \n \n \n \n- \n+ \n \n \n \n \n \n \n \n"}, {"source1": "./usr/share/doc/python-cogent-doc/html/api/__init__/cogent3.__init__.make_unaligned_seqs.html", "source2": "./usr/share/doc/python-cogent-doc/html/api/__init__/cogent3.__init__.make_unaligned_seqs.html", "unified_diff": "@@ -4,26 +4,26 @@\n \n \n \n \n \n \n \n- make_unaligned_seqs — cogent3 2024.11.09 documentation\n+ make_unaligned_seqs — cogent3 2025.12.14 documentation\n \n \n \n \n \n \n \n- \n+ \n \n \n \n \n \n \n \n"}, {"source1": "./usr/share/doc/python-cogent-doc/html/api/__init__/cogent3.__init__.open_.html", "source2": "./usr/share/doc/python-cogent-doc/html/api/__init__/cogent3.__init__.open_.html", "unified_diff": "@@ -4,26 +4,26 @@\n \n \n \n \n \n \n \n- open — cogent3 2024.11.09 documentation\n+ open — cogent3 2025.12.14 documentation\n \n \n \n \n \n \n \n- \n+ \n \n \n \n \n \n \n \n"}, {"source1": "./usr/share/doc/python-cogent-doc/html/api/__init__/cogent3.__init__.open_data_store.html", "source2": "./usr/share/doc/python-cogent-doc/html/api/__init__/cogent3.__init__.open_data_store.html", "unified_diff": "@@ -4,26 +4,26 @@\n \n \n \n \n \n \n \n- open_data_store — cogent3 2024.11.09 documentation\n+ open_data_store — cogent3 2025.12.14 documentation\n \n \n \n \n \n \n \n- \n+ \n \n \n \n \n \n \n \n"}, {"source1": "./usr/share/doc/python-cogent-doc/html/api/alignment/alignment.html", "source2": "./usr/share/doc/python-cogent-doc/html/api/alignment/alignment.html", "unified_diff": "@@ -4,26 +4,26 @@\n \n \n \n \n \n \n \n- alignment — cogent3 2024.11.09 documentation\n+ alignment — cogent3 2025.12.14 documentation\n \n \n \n \n \n \n \n- \n+ \n \n \n \n \n \n \n \n"}, {"source1": "./usr/share/doc/python-cogent-doc/html/api/alignment/classes/cogent3.core.alignment.Alignment.html", "source2": "./usr/share/doc/python-cogent-doc/html/api/alignment/classes/cogent3.core.alignment.Alignment.html", "unified_diff": "@@ -4,26 +4,26 @@\n \n \n \n \n \n \n \n- Alignment — cogent3 2024.11.09 documentation\n+ Alignment — cogent3 2025.12.14 documentation\n \n \n \n \n \n \n \n- \n+ \n \n \n \n \n \n \n \n"}, {"source1": "./usr/share/doc/python-cogent-doc/html/api/alignment/classes/cogent3.core.alignment.ArrayAlignment.html", "source2": "./usr/share/doc/python-cogent-doc/html/api/alignment/classes/cogent3.core.alignment.ArrayAlignment.html", "unified_diff": "@@ -4,26 +4,26 @@\n \n \n \n \n \n \n \n- ArrayAlignment — cogent3 2024.11.09 documentation\n+ ArrayAlignment — cogent3 2025.12.14 documentation\n \n \n \n \n \n \n \n- \n+ \n \n \n \n \n \n \n \n"}, {"source1": "./usr/share/doc/python-cogent-doc/html/api/alignment/classes/cogent3.core.alignment.SequenceCollection.html", "source2": "./usr/share/doc/python-cogent-doc/html/api/alignment/classes/cogent3.core.alignment.SequenceCollection.html", "unified_diff": "@@ -4,26 +4,26 @@\n \n \n \n \n \n \n \n- SequenceCollection — cogent3 2024.11.09 documentation\n+ SequenceCollection — cogent3 2025.12.14 documentation\n \n \n \n \n \n \n \n- \n+ \n \n \n \n \n \n \n \n"}, {"source1": "./usr/share/doc/python-cogent-doc/html/api/alphabet/alphabet.html", "source2": "./usr/share/doc/python-cogent-doc/html/api/alphabet/alphabet.html", "unified_diff": "@@ -4,26 +4,26 @@\n \n \n \n \n \n \n \n- alphabet — cogent3 2024.11.09 documentation\n+ alphabet — cogent3 2025.12.14 documentation\n \n \n \n \n \n \n \n- \n+ \n \n \n \n \n \n \n \n"}, {"source1": "./usr/share/doc/python-cogent-doc/html/api/alphabet/classes/cogent3.core.alphabet.Alphabet.html", "source2": "./usr/share/doc/python-cogent-doc/html/api/alphabet/classes/cogent3.core.alphabet.Alphabet.html", "unified_diff": "@@ -4,26 +4,26 @@\n \n \n \n \n \n \n \n- Alphabet — cogent3 2024.11.09 documentation\n+ Alphabet — cogent3 2025.12.14 documentation\n \n \n \n \n \n \n \n- \n+ \n \n \n \n \n \n \n \n"}, {"source1": "./usr/share/doc/python-cogent-doc/html/api/annotation/annotation.html", "source2": "./usr/share/doc/python-cogent-doc/html/api/annotation/annotation.html", "unified_diff": "@@ -4,26 +4,26 @@\n \n \n \n \n \n \n \n- annotation — cogent3 2024.11.09 documentation\n+ annotation — cogent3 2025.12.14 documentation\n \n \n \n \n \n \n \n- \n+ \n \n \n \n \n \n \n \n"}, {"source1": "./usr/share/doc/python-cogent-doc/html/api/annotation/classes/cogent3.core.annotation.Feature.html", "source2": "./usr/share/doc/python-cogent-doc/html/api/annotation/classes/cogent3.core.annotation.Feature.html", "unified_diff": "@@ -4,26 +4,26 @@\n \n \n \n \n \n \n \n- Feature — cogent3 2024.11.09 documentation\n+ Feature — cogent3 2025.12.14 documentation\n \n \n \n \n \n \n \n- \n+ \n \n \n \n \n \n \n \n"}, {"source1": "./usr/share/doc/python-cogent-doc/html/api/annotation_db/annotation_db.html", "source2": "./usr/share/doc/python-cogent-doc/html/api/annotation_db/annotation_db.html", "unified_diff": "@@ -4,26 +4,26 @@\n \n \n \n \n \n \n \n- annotation_db — cogent3 2024.11.09 documentation\n+ annotation_db — cogent3 2025.12.14 documentation\n \n \n \n \n \n \n \n- \n+ \n \n \n \n \n \n \n \n"}, {"source1": "./usr/share/doc/python-cogent-doc/html/api/annotation_db/classes/cogent3.core.annotation_db.BasicAnnotationDb.html", "source2": "./usr/share/doc/python-cogent-doc/html/api/annotation_db/classes/cogent3.core.annotation_db.BasicAnnotationDb.html", "unified_diff": "@@ -4,26 +4,26 @@\n \n \n \n \n \n \n \n- BasicAnnotationDb — cogent3 2024.11.09 documentation\n+ BasicAnnotationDb — cogent3 2025.12.14 documentation\n \n \n \n \n \n \n \n- \n+ \n \n \n \n \n \n \n \n"}, {"source1": "./usr/share/doc/python-cogent-doc/html/api/annotation_db/classes/cogent3.core.annotation_db.GenbankAnnotationDb.html", "source2": "./usr/share/doc/python-cogent-doc/html/api/annotation_db/classes/cogent3.core.annotation_db.GenbankAnnotationDb.html", "unified_diff": "@@ -4,26 +4,26 @@\n \n \n \n \n \n \n \n- GenbankAnnotationDb — cogent3 2024.11.09 documentation\n+ GenbankAnnotationDb — cogent3 2025.12.14 documentation\n \n \n \n \n \n \n \n- \n+ \n \n \n \n \n \n \n \n"}, {"source1": "./usr/share/doc/python-cogent-doc/html/api/annotation_db/classes/cogent3.core.annotation_db.GffAnnotationDb.html", "source2": "./usr/share/doc/python-cogent-doc/html/api/annotation_db/classes/cogent3.core.annotation_db.GffAnnotationDb.html", "unified_diff": "@@ -4,26 +4,26 @@\n \n \n \n \n \n \n \n- GffAnnotationDb — cogent3 2024.11.09 documentation\n+ GffAnnotationDb — cogent3 2025.12.14 documentation\n \n \n \n \n \n \n \n- \n+ \n \n \n \n \n \n \n \n"}, {"source1": "./usr/share/doc/python-cogent-doc/html/api/app/composable/define_app.html", "source2": "./usr/share/doc/python-cogent-doc/html/api/app/composable/define_app.html", "unified_diff": "@@ -4,26 +4,26 @@\n \n \n \n \n \n \n \n- define_app — cogent3 2024.11.09 documentation\n+ define_app — cogent3 2025.12.14 documentation\n \n \n \n \n \n \n \n- \n+ \n \n \n \n \n \n \n \n"}, {"source1": "./usr/share/doc/python-cogent-doc/html/api/app/data_store/classes/cogent3.app.data_store.DataMember.html", "source2": "./usr/share/doc/python-cogent-doc/html/api/app/data_store/classes/cogent3.app.data_store.DataMember.html", "unified_diff": "@@ -4,26 +4,26 @@\n \n \n \n \n \n \n \n- DataMember — cogent3 2024.11.09 documentation\n+ DataMember — cogent3 2025.12.14 documentation\n \n \n \n \n \n \n \n- \n+ \n \n \n \n \n \n \n \n"}, {"source1": "./usr/share/doc/python-cogent-doc/html/api/app/data_store/classes/cogent3.app.data_store.DataStoreDirectory.html", "source2": "./usr/share/doc/python-cogent-doc/html/api/app/data_store/classes/cogent3.app.data_store.DataStoreDirectory.html", "unified_diff": "@@ -4,26 +4,26 @@\n \n \n \n \n \n \n \n- DataStoreDirectory — cogent3 2024.11.09 documentation\n+ DataStoreDirectory — cogent3 2025.12.14 documentation\n \n \n \n \n \n \n \n- \n+ \n \n \n \n \n \n \n \n"}, {"source1": "./usr/share/doc/python-cogent-doc/html/api/app/data_store/classes/cogent3.app.data_store.ReadOnlyDataStoreZipped.html", "source2": "./usr/share/doc/python-cogent-doc/html/api/app/data_store/classes/cogent3.app.data_store.ReadOnlyDataStoreZipped.html", "unified_diff": "@@ -4,26 +4,26 @@\n \n \n \n \n \n \n \n- ReadOnlyDataStoreZipped — cogent3 2024.11.09 documentation\n+ ReadOnlyDataStoreZipped — cogent3 2025.12.14 documentation\n \n \n \n \n \n \n \n- \n+ \n \n \n \n \n \n \n \n"}, {"source1": "./usr/share/doc/python-cogent-doc/html/api/app/io/classes/cogent3.app.io.register_datastore_reader.html", "source2": "./usr/share/doc/python-cogent-doc/html/api/app/io/classes/cogent3.app.io.register_datastore_reader.html", "unified_diff": "@@ -4,26 +4,26 @@\n \n \n \n \n \n \n \n- register_datastore_reader — cogent3 2024.11.09 documentation\n+ register_datastore_reader — cogent3 2025.12.14 documentation\n \n \n \n \n \n \n \n- \n+ \n \n \n \n \n \n \n \n"}, {"source1": "./usr/share/doc/python-cogent-doc/html/api/app/sqlite_data_store/classes/cogent3.app.sqlite_data_store.DataStoreSqlite.html", "source2": "./usr/share/doc/python-cogent-doc/html/api/app/sqlite_data_store/classes/cogent3.app.sqlite_data_store.DataStoreSqlite.html", "unified_diff": "@@ -4,26 +4,26 @@\n \n \n \n \n \n \n \n- DataStoreSqlite — cogent3 2024.11.09 documentation\n+ DataStoreSqlite — cogent3 2025.12.14 documentation\n \n \n \n \n \n \n \n- \n+ \n \n \n \n \n \n \n \n"}, {"source1": "./usr/share/doc/python-cogent-doc/html/api/genetic_code/classes/cogent3.core.genetic_code.GeneticCode.html", "source2": "./usr/share/doc/python-cogent-doc/html/api/genetic_code/classes/cogent3.core.genetic_code.GeneticCode.html", "unified_diff": "@@ -4,26 +4,26 @@\n \n \n \n \n \n \n \n- GeneticCode — cogent3 2024.11.09 documentation\n+ GeneticCode — cogent3 2025.12.14 documentation\n \n \n \n \n \n \n \n- \n+ \n \n \n \n \n \n \n \n"}, {"source1": "./usr/share/doc/python-cogent-doc/html/api/genetic_code/genetic_code.html", "source2": "./usr/share/doc/python-cogent-doc/html/api/genetic_code/genetic_code.html", "unified_diff": "@@ -4,26 +4,26 @@\n \n \n \n \n \n \n \n- genetic_code — cogent3 2024.11.09 documentation\n+ genetic_code — cogent3 2025.12.14 documentation\n \n \n \n \n \n \n \n- \n+ \n \n \n \n \n \n \n \n"}, {"source1": "./usr/share/doc/python-cogent-doc/html/api/index.html", "source2": "./usr/share/doc/python-cogent-doc/html/api/index.html", "unified_diff": "@@ -4,26 +4,26 @@\n \n \n \n \n \n \n \n- API — cogent3 2024.11.09 documentation\n+ API — cogent3 2025.12.14 documentation\n \n \n \n \n \n \n \n- \n+ \n \n \n \n \n \n \n \n"}, {"source1": "./usr/share/doc/python-cogent-doc/html/api/moltype/classes/cogent3.core.moltype.MolType.html", "source2": "./usr/share/doc/python-cogent-doc/html/api/moltype/classes/cogent3.core.moltype.MolType.html", "unified_diff": "@@ -4,26 +4,26 @@\n \n \n \n \n \n \n \n- MolType — cogent3 2024.11.09 documentation\n+ MolType — cogent3 2025.12.14 documentation\n \n \n \n \n \n \n \n- \n+ \n \n \n \n \n \n \n \n"}, {"source1": "./usr/share/doc/python-cogent-doc/html/api/moltype/moltype.html", "source2": "./usr/share/doc/python-cogent-doc/html/api/moltype/moltype.html", "unified_diff": "@@ -4,26 +4,26 @@\n \n \n \n \n \n \n \n- moltype — cogent3 2024.11.09 documentation\n+ moltype — cogent3 2025.12.14 documentation\n \n \n \n \n \n \n \n- \n+ \n \n \n \n \n \n \n \n"}, {"source1": "./usr/share/doc/python-cogent-doc/html/api/sequence/classes/cogent3.core.sequence.DnaSequence.html", "source2": "./usr/share/doc/python-cogent-doc/html/api/sequence/classes/cogent3.core.sequence.DnaSequence.html", "unified_diff": "@@ -4,26 +4,26 @@\n \n \n \n \n \n \n \n- DnaSequence — cogent3 2024.11.09 documentation\n+ DnaSequence — cogent3 2025.12.14 documentation\n \n \n \n \n \n \n \n- \n+ \n \n \n \n \n \n \n \n"}, {"source1": "./usr/share/doc/python-cogent-doc/html/api/sequence/classes/cogent3.core.sequence.ProteinSequence.html", "source2": "./usr/share/doc/python-cogent-doc/html/api/sequence/classes/cogent3.core.sequence.ProteinSequence.html", "unified_diff": "@@ -4,26 +4,26 @@\n \n \n \n \n \n \n \n- ProteinSequence — cogent3 2024.11.09 documentation\n+ ProteinSequence — cogent3 2025.12.14 documentation\n \n \n \n \n \n \n \n- \n+ \n \n \n \n \n \n \n \n"}, {"source1": "./usr/share/doc/python-cogent-doc/html/api/sequence/classes/cogent3.core.sequence.RnaSequence.html", "source2": "./usr/share/doc/python-cogent-doc/html/api/sequence/classes/cogent3.core.sequence.RnaSequence.html", "unified_diff": "@@ -4,26 +4,26 @@\n \n \n \n \n \n \n \n- RnaSequence — cogent3 2024.11.09 documentation\n+ RnaSequence — cogent3 2025.12.14 documentation\n \n \n \n \n \n \n \n- \n+ \n \n \n \n \n \n \n \n"}, {"source1": "./usr/share/doc/python-cogent-doc/html/api/sequence/sequence.html", "source2": "./usr/share/doc/python-cogent-doc/html/api/sequence/sequence.html", "unified_diff": "@@ -4,26 +4,26 @@\n \n \n \n \n \n \n \n- sequence — cogent3 2024.11.09 documentation\n+ sequence — cogent3 2025.12.14 documentation\n \n \n \n \n \n \n \n- \n+ \n \n \n \n \n \n \n \n"}, {"source1": "./usr/share/doc/python-cogent-doc/html/api/table/classes/cogent3.parse.table.FilteringParser.html", "source2": "./usr/share/doc/python-cogent-doc/html/api/table/classes/cogent3.parse.table.FilteringParser.html", "unified_diff": "@@ -4,26 +4,26 @@\n \n \n \n \n \n \n \n- FilteringParser — cogent3 2024.11.09 documentation\n+ FilteringParser — cogent3 2025.12.14 documentation\n \n \n \n \n \n \n \n- \n+ \n \n \n \n \n \n \n \n"}, {"source1": "./usr/share/doc/python-cogent-doc/html/api/table/classes/cogent3.util.table.Columns.html", "source2": "./usr/share/doc/python-cogent-doc/html/api/table/classes/cogent3.util.table.Columns.html", "unified_diff": "@@ -4,26 +4,26 @@\n \n \n \n \n \n \n \n- Columns — cogent3 2024.11.09 documentation\n+ Columns — cogent3 2025.12.14 documentation\n \n \n \n \n \n \n \n- \n+ \n \n \n \n \n \n \n \n"}, {"source1": "./usr/share/doc/python-cogent-doc/html/api/table/classes/cogent3.util.table.Table.html", "source2": "./usr/share/doc/python-cogent-doc/html/api/table/classes/cogent3.util.table.Table.html", "unified_diff": "@@ -4,26 +4,26 @@\n \n \n \n \n \n \n \n- Table — cogent3 2024.11.09 documentation\n+ Table — cogent3 2025.12.14 documentation\n \n \n \n \n \n \n \n- \n+ \n \n \n \n \n \n \n \n"}, {"source1": "./usr/share/doc/python-cogent-doc/html/api/table/table.html", "source2": "./usr/share/doc/python-cogent-doc/html/api/table/table.html", "unified_diff": "@@ -4,26 +4,26 @@\n \n \n \n \n \n \n \n- table — cogent3 2024.11.09 documentation\n+ table — cogent3 2025.12.14 documentation\n \n \n \n \n \n \n \n- \n+ \n \n \n \n \n \n \n \n"}, {"source1": "./usr/share/doc/python-cogent-doc/html/api/tree/classes/cogent3.core.tree.PhyloNode.html", "source2": "./usr/share/doc/python-cogent-doc/html/api/tree/classes/cogent3.core.tree.PhyloNode.html", "unified_diff": "@@ -4,26 +4,26 @@\n \n \n \n \n \n \n \n- PhyloNode — cogent3 2024.11.09 documentation\n+ PhyloNode — cogent3 2025.12.14 documentation\n \n \n \n \n \n \n \n- \n+ \n \n \n \n \n \n \n \n"}, {"source1": "./usr/share/doc/python-cogent-doc/html/api/tree/tree.html", "source2": "./usr/share/doc/python-cogent-doc/html/api/tree/tree.html", "unified_diff": "@@ -4,26 +4,26 @@\n \n \n \n \n \n \n \n- tree — cogent3 2024.11.09 documentation\n+ tree — cogent3 2025.12.14 documentation\n \n \n \n \n \n \n \n- \n+ \n \n \n \n \n \n \n \n"}, {"source1": "./usr/share/doc/python-cogent-doc/html/api/util/deserialise/classes/cogent3.util.deserialise.register_deserialiser.html", "source2": "./usr/share/doc/python-cogent-doc/html/api/util/deserialise/classes/cogent3.util.deserialise.register_deserialiser.html", "unified_diff": "@@ -4,26 +4,26 @@\n \n \n \n \n \n \n \n- register_deserialiser — cogent3 2024.11.09 documentation\n+ register_deserialiser — cogent3 2025.12.14 documentation\n \n \n \n \n \n \n \n- \n+ \n \n \n \n \n \n \n \n"}, {"source1": "./usr/share/doc/python-cogent-doc/html/api/util/deserialise/deserialise_object.html", "source2": "./usr/share/doc/python-cogent-doc/html/api/util/deserialise/deserialise_object.html", "unified_diff": "@@ -4,26 +4,26 @@\n \n \n \n \n \n \n \n- deserialise_object — cogent3 2024.11.09 documentation\n+ deserialise_object — cogent3 2025.12.14 documentation\n \n \n \n \n \n \n \n- \n+ \n \n \n \n \n \n \n \n"}, {"source1": "./usr/share/doc/python-cogent-doc/html/app/app_cookbook/align-codon.html", "source2": "./usr/share/doc/python-cogent-doc/html/app/app_cookbook/align-codon.html", "unified_diff": "@@ -4,26 +4,26 @@\n \n \n \n \n \n \n \n- Using a codon model — cogent3 2024.11.09 documentation\n+ Using a codon model — cogent3 2025.12.14 documentation\n \n \n \n \n \n \n \n- \n+ \n \n \n \n \n \n \n \n"}, {"source1": "./usr/share/doc/python-cogent-doc/html/app/app_cookbook/align-nucleotide.html", "source2": "./usr/share/doc/python-cogent-doc/html/app/app_cookbook/align-nucleotide.html", "unified_diff": "@@ -4,26 +4,26 @@\n \n \n \n \n \n \n \n- Using a nucleotide model — cogent3 2024.11.09 documentation\n+ Using a nucleotide model — cogent3 2025.12.14 documentation\n \n \n \n \n \n \n \n- \n+ \n \n \n \n \n \n \n \n"}, {"source1": "./usr/share/doc/python-cogent-doc/html/app/app_cookbook/align-protein.html", "source2": "./usr/share/doc/python-cogent-doc/html/app/app_cookbook/align-protein.html", "unified_diff": "@@ -4,26 +4,26 @@\n \n \n \n \n \n \n \n- Using a protein model — cogent3 2024.11.09 documentation\n+ Using a protein model — cogent3 2025.12.14 documentation\n \n \n \n \n \n \n \n- \n+ \n \n \n \n \n \n \n \n"}, {"source1": "./usr/share/doc/python-cogent-doc/html/app/app_cookbook/index-align.html", "source2": "./usr/share/doc/python-cogent-doc/html/app/app_cookbook/index-align.html", "unified_diff": "@@ -4,26 +4,26 @@\n \n \n \n \n \n \n \n- Sequence Alignment — cogent3 2024.11.09 documentation\n+ Sequence Alignment — cogent3 2025.12.14 documentation\n \n \n \n \n \n \n \n- \n+ \n \n \n \n \n \n \n \n"}, {"source1": "./usr/share/doc/python-cogent-doc/html/app/app_cookbook/index-loaders.html", "source2": "./usr/share/doc/python-cogent-doc/html/app/app_cookbook/index-loaders.html", "unified_diff": "@@ -4,26 +4,26 @@\n \n \n \n \n \n \n \n- Loading data — cogent3 2024.11.09 documentation\n+ Loading data — cogent3 2025.12.14 documentation\n \n \n \n \n \n \n \n- \n+ \n \n \n \n \n \n \n \n"}, {"source1": "./usr/share/doc/python-cogent-doc/html/app/app_cookbook/index-sample.html", "source2": "./usr/share/doc/python-cogent-doc/html/app/app_cookbook/index-sample.html", "unified_diff": "@@ -4,26 +4,26 @@\n \n \n \n \n \n \n \n- Filtering data — cogent3 2024.11.09 documentation\n+ Filtering data — cogent3 2025.12.14 documentation\n \n \n \n \n \n \n \n- \n+ \n \n \n \n \n \n \n \n"}, {"source1": "./usr/share/doc/python-cogent-doc/html/app/app_cookbook/index-writers.html", "source2": "./usr/share/doc/python-cogent-doc/html/app/app_cookbook/index-writers.html", "unified_diff": "@@ -4,26 +4,26 @@\n \n \n \n \n \n \n \n- Writing Data — cogent3 2024.11.09 documentation\n+ Writing Data — cogent3 2025.12.14 documentation\n \n \n \n \n \n \n \n- \n+ \n \n \n \n \n \n \n \n"}, {"source1": "./usr/share/doc/python-cogent-doc/html/app/app_cookbook/load-aligned.html", "source2": "./usr/share/doc/python-cogent-doc/html/app/app_cookbook/load-aligned.html", "unified_diff": "@@ -4,26 +4,26 @@\n \n \n \n \n \n \n \n- Loading aligned sequence data — cogent3 2024.11.09 documentation\n+ Loading aligned sequence data — cogent3 2025.12.14 documentation\n \n \n \n \n \n \n \n- \n+ \n \n \n \n \n \n \n \n"}, {"source1": "./usr/share/doc/python-cogent-doc/html/app/app_cookbook/load-json.html", "source2": "./usr/share/doc/python-cogent-doc/html/app/app_cookbook/load-json.html", "unified_diff": "@@ -4,26 +4,26 @@\n \n \n \n \n \n \n \n- Loading JSON serialised objects — cogent3 2024.11.09 documentation\n+ Loading JSON serialised objects — cogent3 2025.12.14 documentation\n \n \n \n \n \n \n \n- \n+ \n \n \n \n \n \n \n \n"}, {"source1": "./usr/share/doc/python-cogent-doc/html/app/app_cookbook/load-tabular.html", "source2": "./usr/share/doc/python-cogent-doc/html/app/app_cookbook/load-tabular.html", "unified_diff": "@@ -4,26 +4,26 @@\n \n \n \n \n \n \n \n- Loading tabular data — cogent3 2024.11.09 documentation\n+ Loading tabular data — cogent3 2025.12.14 documentation\n \n \n \n \n \n \n \n- \n+ \n \n \n \n \n \n \n \n"}, {"source1": "./usr/share/doc/python-cogent-doc/html/app/app_cookbook/load-unaligned.html", "source2": "./usr/share/doc/python-cogent-doc/html/app/app_cookbook/load-unaligned.html", "unified_diff": "@@ -4,26 +4,26 @@\n \n \n \n \n \n \n \n- Loading unaligned sequence data — cogent3 2024.11.09 documentation\n+ Loading unaligned sequence data — cogent3 2025.12.14 documentation\n \n \n \n \n \n \n \n- \n+ \n \n \n \n \n \n \n \n"}, {"source1": "./usr/share/doc/python-cogent-doc/html/app/app_cookbook/sample-concat.html", "source2": "./usr/share/doc/python-cogent-doc/html/app/app_cookbook/sample-concat.html", "unified_diff": "@@ -4,26 +4,26 @@\n \n \n \n \n \n \n \n- Concatenating alignments — cogent3 2024.11.09 documentation\n+ Concatenating alignments — cogent3 2025.12.14 documentation\n \n \n \n \n \n \n \n- \n+ \n \n \n \n \n \n \n \n"}, {"source1": "./usr/share/doc/python-cogent-doc/html/app/app_cookbook/sample-fixed-len.html", "source2": "./usr/share/doc/python-cogent-doc/html/app/app_cookbook/sample-fixed-len.html", "unified_diff": "@@ -4,26 +4,26 @@\n \n \n \n \n \n \n \n- Sample an alignment to a fixed length — cogent3 2024.11.09 documentation\n+ Sample an alignment to a fixed length — cogent3 2025.12.14 documentation\n \n \n \n \n \n \n \n- \n+ \n \n \n \n \n \n \n \n"}, {"source1": "./usr/share/doc/python-cogent-doc/html/app/app_cookbook/sample-min-len.html", "source2": "./usr/share/doc/python-cogent-doc/html/app/app_cookbook/sample-min-len.html", "unified_diff": "@@ -4,26 +4,26 @@\n \n \n \n \n \n \n \n- Filter sequence collections and alignments by length — cogent3 2024.11.09 documentation\n+ Filter sequence collections and alignments by length — cogent3 2025.12.14 documentation\n \n \n \n \n \n \n \n- \n+ \n \n \n \n \n \n \n \n"}, {"source1": "./usr/share/doc/python-cogent-doc/html/app/app_cookbook/sample-omit-bad.html", "source2": "./usr/share/doc/python-cogent-doc/html/app/app_cookbook/sample-omit-bad.html", "unified_diff": "@@ -4,26 +4,26 @@\n \n \n \n \n \n \n \n- Remove problem sequences from an alignment — cogent3 2024.11.09 documentation\n+ Remove problem sequences from an alignment — cogent3 2025.12.14 documentation\n \n \n \n \n \n \n \n- \n+ \n \n \n \n \n \n \n \n"}, {"source1": "./usr/share/doc/python-cogent-doc/html/app/app_cookbook/sample-omit-degen.html", "source2": "./usr/share/doc/python-cogent-doc/html/app/app_cookbook/sample-omit-degen.html", "unified_diff": "@@ -4,26 +4,26 @@\n \n \n \n \n \n \n \n- Removing degenerate characters — cogent3 2024.11.09 documentation\n+ Removing degenerate characters — cogent3 2025.12.14 documentation\n \n \n \n \n \n \n \n- \n+ \n \n \n \n \n \n \n \n"}, {"source1": "./usr/share/doc/python-cogent-doc/html/app/app_cookbook/sample-omit-duplicated.html", "source2": "./usr/share/doc/python-cogent-doc/html/app/app_cookbook/sample-omit-duplicated.html", "unified_diff": "@@ -4,26 +4,26 @@\n \n \n \n \n \n \n \n- Remove duplicated sequences from an alignment — cogent3 2024.11.09 documentation\n+ Remove duplicated sequences from an alignment — cogent3 2025.12.14 documentation\n \n \n \n \n \n \n \n- \n+ \n \n \n \n \n \n \n \n"}, {"source1": "./usr/share/doc/python-cogent-doc/html/app/app_cookbook/sample-omit-gap.html", "source2": "./usr/share/doc/python-cogent-doc/html/app/app_cookbook/sample-omit-gap.html", "unified_diff": "@@ -4,26 +4,26 @@\n \n \n \n \n \n \n \n- Removing highly gapped positions — cogent3 2024.11.09 documentation\n+ Removing highly gapped positions — cogent3 2025.12.14 documentation\n \n \n \n \n \n \n \n- \n+ \n \n \n \n \n \n \n \n"}, {"source1": "./usr/share/doc/python-cogent-doc/html/app/app_cookbook/sample-take-n-seqs.html", "source2": "./usr/share/doc/python-cogent-doc/html/app/app_cookbook/sample-take-n-seqs.html", "unified_diff": "@@ -4,26 +4,26 @@\n \n \n \n \n \n \n \n- Select n sequences from a collection — cogent3 2024.11.09 documentation\n+ Select n sequences from a collection — cogent3 2025.12.14 documentation\n \n \n \n \n \n \n \n- \n+ \n \n \n \n \n \n \n \n"}, {"source1": "./usr/share/doc/python-cogent-doc/html/app/app_cookbook/sample-take-pos.html", "source2": "./usr/share/doc/python-cogent-doc/html/app/app_cookbook/sample-take-pos.html", "unified_diff": "@@ -4,26 +4,26 @@\n \n \n \n \n \n \n \n- Sample nucleotides from a given codon position — cogent3 2024.11.09 documentation\n+ Sample nucleotides from a given codon position — cogent3 2025.12.14 documentation\n \n \n \n \n \n \n \n- \n+ \n \n \n \n \n \n \n \n"}, {"source1": "./usr/share/doc/python-cogent-doc/html/app/app_cookbook/sample-take-seqs.html", "source2": "./usr/share/doc/python-cogent-doc/html/app/app_cookbook/sample-take-seqs.html", "unified_diff": "@@ -4,26 +4,26 @@\n \n \n \n \n \n \n \n- Select named sequences from a collection — cogent3 2024.11.09 documentation\n+ Select named sequences from a collection — cogent3 2025.12.14 documentation\n \n \n \n \n \n \n \n- \n+ \n \n \n \n \n \n \n \n"}, {"source1": "./usr/share/doc/python-cogent-doc/html/app/app_cookbook/sample-trim-stops.html", "source2": "./usr/share/doc/python-cogent-doc/html/app/app_cookbook/sample-trim-stops.html", "unified_diff": "@@ -4,26 +4,26 @@\n \n \n \n \n \n \n \n- Remove trailing stop codons from sequences in an alignment — cogent3 2024.11.09 documentation\n+ Remove trailing stop codons from sequences in an alignment — cogent3 2025.12.14 documentation\n \n \n \n \n \n \n \n- \n+ \n \n \n \n \n \n \n \n"}, {"source1": "./usr/share/doc/python-cogent-doc/html/app/app_cookbook/write-db.html", "source2": "./usr/share/doc/python-cogent-doc/html/app/app_cookbook/write-db.html", "unified_diff": "@@ -4,26 +4,26 @@\n \n \n \n \n \n \n \n- Writing a database to file — cogent3 2024.11.09 documentation\n+ Writing a database to file — cogent3 2025.12.14 documentation\n \n \n \n \n \n \n \n- \n+ \n \n \n \n \n \n \n \n"}, {"source1": "./usr/share/doc/python-cogent-doc/html/app/app_cookbook/write-json.html", "source2": "./usr/share/doc/python-cogent-doc/html/app/app_cookbook/write-json.html", "unified_diff": "@@ -4,26 +4,26 @@\n \n \n \n \n \n \n \n- Writing JSON Serialised Objects — cogent3 2024.11.09 documentation\n+ Writing JSON Serialised Objects — cogent3 2025.12.14 documentation\n \n \n \n \n \n \n \n- \n+ \n \n \n \n \n \n \n \n"}, {"source1": "./usr/share/doc/python-cogent-doc/html/app/app_cookbook/write-seqs.html", "source2": "./usr/share/doc/python-cogent-doc/html/app/app_cookbook/write-seqs.html", "unified_diff": "@@ -4,26 +4,26 @@\n \n \n \n \n \n \n \n- Writing sequences and sequence alignments — cogent3 2024.11.09 documentation\n+ Writing sequences and sequence alignments — cogent3 2025.12.14 documentation\n \n \n \n \n \n \n \n- \n+ \n \n \n \n \n \n \n \n"}, {"source1": "./usr/share/doc/python-cogent-doc/html/app/app_cookbook/write-tabular.html", "source2": "./usr/share/doc/python-cogent-doc/html/app/app_cookbook/write-tabular.html", "unified_diff": "@@ -4,26 +4,26 @@\n \n \n \n \n \n \n \n- Writing tabular data — cogent3 2024.11.09 documentation\n+ Writing tabular data — cogent3 2025.12.14 documentation\n \n \n \n \n \n \n \n- \n+ \n \n \n \n \n \n \n \n"}, {"source1": "./usr/share/doc/python-cogent-doc/html/app/app_overview/app-get.html", "source2": "./usr/share/doc/python-cogent-doc/html/app/app_overview/app-get.html", "unified_diff": "@@ -4,26 +4,26 @@\n \n \n \n \n \n \n \n- Getting an app — cogent3 2024.11.09 documentation\n+ Getting an app — cogent3 2025.12.14 documentation\n \n \n \n \n \n \n \n- \n+ \n \n \n \n \n \n \n \n"}, {"source1": "./usr/share/doc/python-cogent-doc/html/app/app_overview/app-help.html", "source2": "./usr/share/doc/python-cogent-doc/html/app/app_overview/app-help.html", "unified_diff": "@@ -4,26 +4,26 @@\n \n \n \n \n \n \n \n- Getting help on an app — cogent3 2024.11.09 documentation\n+ Getting help on an app — cogent3 2025.12.14 documentation\n \n \n \n \n \n \n \n- \n+ \n \n \n \n \n \n \n \n"}, {"source1": "./usr/share/doc/python-cogent-doc/html/app/app_overview/app-overview.html", "source2": "./usr/share/doc/python-cogent-doc/html/app/app_overview/app-overview.html", "unified_diff": "@@ -4,26 +4,26 @@\n \n \n \n \n \n \n \n- Overview of using apps — cogent3 2024.11.09 documentation\n+ Overview of using apps — cogent3 2025.12.14 documentation\n \n \n \n \n \n \n \n- \n+ \n \n \n \n \n \n \n \n"}, {"source1": "./usr/share/doc/python-cogent-doc/html/app/app_overview/available-apps.html", "source2": "./usr/share/doc/python-cogent-doc/html/app/app_overview/available-apps.html", "unified_diff": "@@ -4,26 +4,26 @@\n \n \n \n \n \n \n \n- Displaying installed apps — cogent3 2024.11.09 documentation\n+ Displaying installed apps — cogent3 2025.12.14 documentation\n \n \n \n \n \n \n \n- \n+ \n \n \n \n \n \n \n \n"}, {"source1": "./usr/share/doc/python-cogent-doc/html/app/app_overview/dstore.html", "source2": "./usr/share/doc/python-cogent-doc/html/app/app_overview/dstore.html", "unified_diff": "@@ -4,26 +4,26 @@\n \n \n \n \n \n \n \n- Data stores \u2013 collections of data records — cogent3 2024.11.09 documentation\n+ Data stores \u2013 collections of data records — cogent3 2025.12.14 documentation\n \n \n \n \n \n \n \n- \n+ \n \n \n \n \n \n \n \n"}, {"source1": "./usr/share/doc/python-cogent-doc/html/app/app_overview/not-completed.html", "source2": "./usr/share/doc/python-cogent-doc/html/app/app_overview/not-completed.html", "unified_diff": "@@ -4,26 +4,26 @@\n \n \n \n \n \n \n \n- Tracking records that could not be processed — cogent3 2024.11.09 documentation\n+ Tracking records that could not be processed — cogent3 2025.12.14 documentation\n \n \n \n \n \n \n \n- \n+ \n \n \n \n \n \n \n \n"}, {"source1": "./usr/share/doc/python-cogent-doc/html/app/app_tutorials/evo-ancestral-states.html", "source2": "./usr/share/doc/python-cogent-doc/html/app/app_tutorials/evo-ancestral-states.html", "unified_diff": "@@ -4,26 +4,26 @@\n \n \n \n \n \n \n \n- Reconstructing ancestral states — cogent3 2024.11.09 documentation\n+ Reconstructing ancestral states — cogent3 2025.12.14 documentation\n \n \n \n \n \n \n \n- \n+ \n \n \n \n \n \n \n \n"}, {"source1": "./usr/share/doc/python-cogent-doc/html/app/app_tutorials/evo-dt-nuc-model.html", "source2": "./usr/share/doc/python-cogent-doc/html/app/app_tutorials/evo-dt-nuc-model.html", "unified_diff": "@@ -4,26 +4,26 @@\n \n \n \n \n \n \n \n- Applying a discrete-time, non-stationary nucleotide model — cogent3 2024.11.09 documentation\n+ Applying a discrete-time, non-stationary nucleotide model — cogent3 2025.12.14 documentation\n \n \n \n \n \n \n \n- \n+ \n \n \n \n \n \n \n \n"}, {"source1": "./usr/share/doc/python-cogent-doc/html/app/app_tutorials/evo-extract-model-stats.html", "source2": "./usr/share/doc/python-cogent-doc/html/app/app_tutorials/evo-extract-model-stats.html", "unified_diff": "@@ -4,26 +4,26 @@\n \n \n \n \n \n \n \n- Extracting maximum likelihood estimates from a model_result — cogent3 2024.11.09 documentation\n+ Extracting maximum likelihood estimates from a model_result — cogent3 2025.12.14 documentation\n \n \n \n \n \n \n \n- \n+ \n \n \n \n \n \n \n \n"}, {"source1": "./usr/share/doc/python-cogent-doc/html/app/app_tutorials/evo-hypothesis.html", "source2": "./usr/share/doc/python-cogent-doc/html/app/app_tutorials/evo-hypothesis.html", "unified_diff": "@@ -4,26 +4,26 @@\n \n \n \n \n \n \n \n- Testing a hypothesis \u2013 non-stationary or time-reversible — cogent3 2024.11.09 documentation\n+ Testing a hypothesis \u2013 non-stationary or time-reversible — cogent3 2025.12.14 documentation\n \n \n \n \n \n \n \n- \n+ \n \n \n \n \n \n \n \n"}, {"source1": "./usr/share/doc/python-cogent-doc/html/app/app_tutorials/evo-model-timehet.html", "source2": "./usr/share/doc/python-cogent-doc/html/app/app_tutorials/evo-model-timehet.html", "unified_diff": "@@ -4,26 +4,26 @@\n \n \n \n \n \n \n \n- Specifying a non-stationary model with time-heterogeneous parameters — cogent3 2024.11.09 documentation\n+ Specifying a non-stationary model with time-heterogeneous parameters — cogent3 2025.12.14 documentation\n \n \n \n \n \n \n \n- \n+ \n \n \n \n \n \n \n \n"}, {"source1": "./usr/share/doc/python-cogent-doc/html/app/app_tutorials/evo-model-with-tree.html", "source2": "./usr/share/doc/python-cogent-doc/html/app/app_tutorials/evo-model-with-tree.html", "unified_diff": "@@ -4,26 +4,26 @@\n \n \n \n \n \n \n \n- Apply a non-stationary nucleotide model to an alignment with a tree — cogent3 2024.11.09 documentation\n+ Apply a non-stationary nucleotide model to an alignment with a tree — cogent3 2025.12.14 documentation\n \n \n \n \n \n \n \n- \n+ \n \n \n \n \n \n \n \n"}, {"source1": "./usr/share/doc/python-cogent-doc/html/app/app_tutorials/evo-model.html", "source2": "./usr/share/doc/python-cogent-doc/html/app/app_tutorials/evo-model.html", "unified_diff": "@@ -4,26 +4,26 @@\n \n \n \n \n \n \n \n- Apply a non-stationary nucleotide model to an alignment with 3 sequences — cogent3 2024.11.09 documentation\n+ Apply a non-stationary nucleotide model to an alignment with 3 sequences — cogent3 2025.12.14 documentation\n \n \n \n \n \n \n \n- \n+ \n \n \n \n \n \n \n \n"}, {"source1": "./usr/share/doc/python-cogent-doc/html/app/app_tutorials/evo-natsel_neutral.html", "source2": "./usr/share/doc/python-cogent-doc/html/app/app_tutorials/evo-natsel_neutral.html", "unified_diff": "@@ -4,26 +4,26 @@\n \n \n \n \n \n \n \n- natsel_neutral \u2013 a test for selective neutrality — cogent3 2024.11.09 documentation\n+ natsel_neutral \u2013 a test for selective neutrality — cogent3 2025.12.14 documentation\n \n \n \n \n \n \n \n- \n+ \n \n \n \n \n \n \n \n"}, {"source1": "./usr/share/doc/python-cogent-doc/html/app/app_tutorials/evo-natsel_sitehet.html", "source2": "./usr/share/doc/python-cogent-doc/html/app/app_tutorials/evo-natsel_sitehet.html", "unified_diff": "@@ -4,26 +4,26 @@\n \n \n \n \n \n \n \n- natsel_sitehet \u2013 a test of site heterogeneity — cogent3 2024.11.09 documentation\n+ natsel_sitehet \u2013 a test of site heterogeneity — cogent3 2025.12.14 documentation\n \n \n \n \n \n \n \n- \n+ \n \n \n \n \n \n \n \n"}, {"source1": "./usr/share/doc/python-cogent-doc/html/app/app_tutorials/evo-natsel_timehet.html", "source2": "./usr/share/doc/python-cogent-doc/html/app/app_tutorials/evo-natsel_timehet.html", "unified_diff": "@@ -4,26 +4,26 @@\n \n \n \n \n \n \n \n- natsel_timehet \u2013 a test of branch heterogeneity — cogent3 2024.11.09 documentation\n+ natsel_timehet \u2013 a test of branch heterogeneity — cogent3 2025.12.14 documentation\n \n \n \n \n \n \n \n- \n+ \n \n \n \n \n \n \n \n"}, {"source1": "./usr/share/doc/python-cogent-doc/html/app/app_tutorials/evo-natsel_zhang.html", "source2": "./usr/share/doc/python-cogent-doc/html/app/app_tutorials/evo-natsel_zhang.html", "unified_diff": "@@ -4,26 +4,26 @@\n \n \n \n \n \n \n \n- natsel_zhang \u2013 a branch-site test — cogent3 2024.11.09 documentation\n+ natsel_zhang \u2013 a branch-site test — cogent3 2025.12.14 documentation\n \n \n \n \n \n \n \n- \n+ \n \n \n \n \n \n \n \n"}, {"source1": "./usr/share/doc/python-cogent-doc/html/app/app_tutorials/evo-nstat-codon-model.html", "source2": "./usr/share/doc/python-cogent-doc/html/app/app_tutorials/evo-nstat-codon-model.html", "unified_diff": "@@ -4,26 +4,26 @@\n \n \n \n \n \n \n \n- Applying GNC, a non-stationary codon model — cogent3 2024.11.09 documentation\n+ Applying GNC, a non-stationary codon model — cogent3 2025.12.14 documentation\n \n \n \n \n \n \n \n- \n+ \n \n \n \n \n \n \n \n"}, {"source1": "./usr/share/doc/python-cogent-doc/html/app/app_tutorials/evo-tr-codon-model.html", "source2": "./usr/share/doc/python-cogent-doc/html/app/app_tutorials/evo-tr-codon-model.html", "unified_diff": "@@ -4,26 +4,26 @@\n \n \n \n \n \n \n \n- Applying a time-reversible codon model — cogent3 2024.11.09 documentation\n+ Applying a time-reversible codon model — cogent3 2025.12.14 documentation\n \n \n \n \n \n \n \n- \n+ \n \n \n \n \n \n \n \n"}, {"source1": "./usr/share/doc/python-cogent-doc/html/app/app_tutorials/evo-tr-nuc-model.html", "source2": "./usr/share/doc/python-cogent-doc/html/app/app_tutorials/evo-tr-nuc-model.html", "unified_diff": "@@ -4,26 +4,26 @@\n \n \n \n \n \n \n \n- Applying a time-reversible nucleotide model — cogent3 2024.11.09 documentation\n+ Applying a time-reversible nucleotide model — cogent3 2025.12.14 documentation\n \n \n \n \n \n \n \n- \n+ \n \n \n \n \n \n \n \n"}, {"source1": "./usr/share/doc/python-cogent-doc/html/app/app_tutorials/index-evo-hypothesis.html", "source2": "./usr/share/doc/python-cogent-doc/html/app/app_tutorials/index-evo-hypothesis.html", "unified_diff": "@@ -4,26 +4,26 @@\n \n \n \n \n \n \n \n- Testing hypotheses about sequence evolution — cogent3 2024.11.09 documentation\n+ Testing hypotheses about sequence evolution — cogent3 2025.12.14 documentation\n \n \n \n \n \n \n \n- \n+ \n \n \n \n \n \n \n \n"}, {"source1": "./usr/share/doc/python-cogent-doc/html/app/app_tutorials/index-evo-model.html", "source2": "./usr/share/doc/python-cogent-doc/html/app/app_tutorials/index-evo-model.html", "unified_diff": "@@ -4,26 +4,26 @@\n \n \n \n \n \n \n \n- Modelling sequence evolution — cogent3 2024.11.09 documentation\n+ Modelling sequence evolution — cogent3 2025.12.14 documentation\n \n \n \n \n \n \n \n- \n+ \n \n \n \n \n \n \n \n"}, {"source1": "./usr/share/doc/python-cogent-doc/html/app/app_tutorials/index-evo-natsel.html", "source2": "./usr/share/doc/python-cogent-doc/html/app/app_tutorials/index-evo-natsel.html", "unified_diff": "@@ -4,26 +4,26 @@\n \n \n \n \n \n \n \n- Testing for natural selection — cogent3 2024.11.09 documentation\n+ Testing for natural selection — cogent3 2025.12.14 documentation\n \n \n \n \n \n \n \n- \n+ \n \n \n \n \n \n \n \n"}, {"source1": "./usr/share/doc/python-cogent-doc/html/app/index-app.html", "source2": "./usr/share/doc/python-cogent-doc/html/app/index-app.html", "unified_diff": "@@ -4,26 +4,26 @@\n \n \n \n \n \n \n \n- Overview of apps — cogent3 2024.11.09 documentation\n+ Overview of apps — cogent3 2025.12.14 documentation\n \n \n \n \n \n \n \n- \n+ \n \n \n \n \n \n \n \n"}, {"source1": "./usr/share/doc/python-cogent-doc/html/app/index-cookbook.html", "source2": "./usr/share/doc/python-cogent-doc/html/app/index-cookbook.html", "unified_diff": "@@ -4,26 +4,26 @@\n \n \n \n \n \n \n \n- App Cookbook — cogent3 2024.11.09 documentation\n+ App Cookbook — cogent3 2025.12.14 documentation\n \n \n \n \n \n \n \n- \n+ \n \n \n \n \n \n \n \n"}, {"source1": "./usr/share/doc/python-cogent-doc/html/app/index-custom.html", "source2": "./usr/share/doc/python-cogent-doc/html/app/index-custom.html", "unified_diff": "@@ -4,26 +4,26 @@\n \n \n \n \n \n \n \n- Custom Apps — cogent3 2024.11.09 documentation\n+ Custom Apps — cogent3 2025.12.14 documentation\n \n \n \n \n \n \n \n- \n+ \n \n \n \n \n \n \n \n"}, {"source1": "./usr/share/doc/python-cogent-doc/html/app/index-help.html", "source2": "./usr/share/doc/python-cogent-doc/html/app/index-help.html", "unified_diff": "@@ -4,26 +4,26 @@\n \n \n \n \n \n \n \n- <no title> — cogent3 2024.11.09 documentation\n+ <no title> — cogent3 2025.12.14 documentation\n \n \n \n \n \n \n \n- \n+ \n \n \n \n \n \n \n \n"}, {"source1": "./usr/share/doc/python-cogent-doc/html/app/index-tutorials.html", "source2": "./usr/share/doc/python-cogent-doc/html/app/index-tutorials.html", "unified_diff": "@@ -4,26 +4,26 @@\n \n \n \n \n \n \n \n- Tutorials — cogent3 2024.11.09 documentation\n+ Tutorials — cogent3 2025.12.14 documentation\n \n \n \n \n \n \n \n- \n+ \n \n \n \n \n \n \n \n"}, {"source1": "./usr/share/doc/python-cogent-doc/html/app/index.html", "source2": "./usr/share/doc/python-cogent-doc/html/app/index.html", "unified_diff": "@@ -4,26 +4,26 @@\n \n \n \n \n \n \n \n- apps — cogent3 2024.11.09 documentation\n+ apps — cogent3 2025.12.14 documentation\n \n \n \n \n \n \n \n- \n+ \n \n \n \n \n \n \n \n"}, {"source1": "./usr/share/doc/python-cogent-doc/html/app/user_function.html", "source2": "./usr/share/doc/python-cogent-doc/html/app/user_function.html", "unified_diff": "@@ -4,26 +4,26 @@\n \n \n \n \n \n \n \n- Turn your functions into composable apps — cogent3 2024.11.09 documentation\n+ Turn your functions into composable apps — cogent3 2025.12.14 documentation\n \n \n \n \n \n \n \n- \n+ \n \n \n \n \n \n \n \n"}, {"source1": "./usr/share/doc/python-cogent-doc/html/community.html", "source2": "./usr/share/doc/python-cogent-doc/html/community.html", "unified_diff": "@@ -4,26 +4,26 @@\n \n \n \n \n \n \n \n- Community — cogent3 2024.11.09 documentation\n+ Community — cogent3 2025.12.14 documentation\n \n \n \n \n \n \n \n- \n+ \n \n \n \n \n \n \n \n"}, {"source1": "./usr/share/doc/python-cogent-doc/html/cookbook/DNA_and_RNA_sequences.html", "source2": "./usr/share/doc/python-cogent-doc/html/cookbook/DNA_and_RNA_sequences.html", "unified_diff": "@@ -4,26 +4,26 @@\n \n \n \n \n \n \n \n- Sequences — cogent3 2024.11.09 documentation\n+ Sequences — cogent3 2025.12.14 documentation\n \n \n \n \n \n \n \n- \n+ \n \n \n \n \n \n \n \n"}, {"source1": "./usr/share/doc/python-cogent-doc/html/cookbook/alignments.html", "source2": "./usr/share/doc/python-cogent-doc/html/cookbook/alignments.html", "unified_diff": "@@ -4,26 +4,26 @@\n \n \n \n \n \n \n \n- Sequence Collections and Alignments — cogent3 2024.11.09 documentation\n+ Sequence Collections and Alignments — cogent3 2025.12.14 documentation\n \n \n \n \n \n \n \n- \n+ \n \n \n \n \n \n \n \n"}, {"source1": "./usr/share/doc/python-cogent-doc/html/cookbook/alphabet.html", "source2": "./usr/share/doc/python-cogent-doc/html/cookbook/alphabet.html", "unified_diff": "@@ -4,26 +4,26 @@\n \n \n \n \n \n \n \n- Alphabets — cogent3 2024.11.09 documentation\n+ Alphabets — cogent3 2025.12.14 documentation\n \n \n \n \n \n \n \n- \n+ \n \n \n \n \n \n \n \n"}, {"source1": "./usr/share/doc/python-cogent-doc/html/cookbook/annotation_db.html", "source2": "./usr/share/doc/python-cogent-doc/html/cookbook/annotation_db.html", "unified_diff": "@@ -4,26 +4,26 @@\n \n \n \n \n \n \n \n- Annotation Databases — cogent3 2024.11.09 documentation\n+ Annotation Databases — cogent3 2025.12.14 documentation\n \n \n \n \n \n \n \n- \n+ \n \n \n \n \n \n \n \n"}, {"source1": "./usr/share/doc/python-cogent-doc/html/cookbook/building_alignments.html", "source2": "./usr/share/doc/python-cogent-doc/html/cookbook/building_alignments.html", "unified_diff": "@@ -4,26 +4,26 @@\n \n \n \n \n \n \n \n- Building alignments — cogent3 2024.11.09 documentation\n+ Building alignments — cogent3 2025.12.14 documentation\n \n \n \n \n \n \n \n- \n+ \n \n \n \n \n \n \n \n"}, {"source1": "./usr/share/doc/python-cogent-doc/html/cookbook/building_phylogenies.html", "source2": "./usr/share/doc/python-cogent-doc/html/cookbook/building_phylogenies.html", "unified_diff": "@@ -4,26 +4,26 @@\n \n \n \n \n \n \n \n- Building phylogenies — cogent3 2024.11.09 documentation\n+ Building phylogenies — cogent3 2025.12.14 documentation\n \n \n \n \n \n \n \n- \n+ \n \n \n \n \n \n \n \n"}, {"source1": "./usr/share/doc/python-cogent-doc/html/cookbook/calc_genetic_distance.html", "source2": "./usr/share/doc/python-cogent-doc/html/cookbook/calc_genetic_distance.html", "unified_diff": "@@ -4,26 +4,26 @@\n \n \n \n \n \n \n \n- Genetic distance calculation — cogent3 2024.11.09 documentation\n+ Genetic distance calculation — cogent3 2025.12.14 documentation\n \n \n \n \n \n \n \n- \n+ \n \n \n \n \n \n \n \n"}, {"source1": "./usr/share/doc/python-cogent-doc/html/cookbook/evo_modelling.html", "source2": "./usr/share/doc/python-cogent-doc/html/cookbook/evo_modelling.html", "unified_diff": "@@ -4,26 +4,26 @@\n \n \n \n \n \n \n \n- Evolutionary Analysis Using Likelihood — cogent3 2024.11.09 documentation\n+ Evolutionary Analysis Using Likelihood — cogent3 2025.12.14 documentation\n \n \n \n \n \n \n \n- \n+ \n \n \n \n \n \n \n \n"}, {"source1": "./usr/share/doc/python-cogent-doc/html/cookbook/features.html", "source2": "./usr/share/doc/python-cogent-doc/html/cookbook/features.html", "unified_diff": "@@ -4,26 +4,26 @@\n \n \n \n \n \n \n \n- Features — cogent3 2024.11.09 documentation\n+ Features — cogent3 2025.12.14 documentation\n \n \n \n \n \n \n \n- \n+ \n \n \n \n \n \n \n \n"}, {"source1": "./usr/share/doc/python-cogent-doc/html/cookbook/genetic_code.html", "source2": "./usr/share/doc/python-cogent-doc/html/cookbook/genetic_code.html", "unified_diff": "@@ -4,26 +4,26 @@\n \n \n \n \n \n \n \n- Using genetic codes — cogent3 2024.11.09 documentation\n+ Using genetic codes — cogent3 2025.12.14 documentation\n \n \n \n \n \n \n \n- \n+ \n \n \n \n \n \n \n \n"}, {"source1": "./usr/share/doc/python-cogent-doc/html/cookbook/index.html", "source2": "./usr/share/doc/python-cogent-doc/html/cookbook/index.html", "unified_diff": "@@ -4,26 +4,26 @@\n \n \n \n \n \n \n \n- Cookbook — cogent3 2024.11.09 documentation\n+ Cookbook — cogent3 2025.12.14 documentation\n \n \n \n \n \n \n \n- \n+ \n \n \n \n \n \n \n \n"}, {"source1": "./usr/share/doc/python-cogent-doc/html/cookbook/loading_sequences.html", "source2": "./usr/share/doc/python-cogent-doc/html/cookbook/loading_sequences.html", "unified_diff": "@@ -4,26 +4,26 @@\n \n \n \n \n \n \n \n- Loading a sequence from a file — cogent3 2024.11.09 documentation\n+ Loading a sequence from a file — cogent3 2025.12.14 documentation\n \n \n \n \n \n \n \n- \n+ \n \n \n \n \n \n \n \n"}, {"source1": "./usr/share/doc/python-cogent-doc/html/cookbook/loading_tabular.html", "source2": "./usr/share/doc/python-cogent-doc/html/cookbook/loading_tabular.html", "unified_diff": "@@ -4,26 +4,26 @@\n \n \n \n \n \n \n \n- Loading a csv file — cogent3 2024.11.09 documentation\n+ Loading a csv file — cogent3 2025.12.14 documentation\n \n \n \n \n \n \n \n- \n+ \n \n \n \n \n \n \n \n"}, {"source1": "./usr/share/doc/python-cogent-doc/html/cookbook/manipulating_biological_data.html", "source2": "./usr/share/doc/python-cogent-doc/html/cookbook/manipulating_biological_data.html", "unified_diff": "@@ -4,26 +4,26 @@\n \n \n \n \n \n \n \n- Manipulating biological data — cogent3 2024.11.09 documentation\n+ Manipulating biological data — cogent3 2025.12.14 documentation\n \n \n \n \n \n \n \n- \n+ \n \n \n \n \n \n \n \n"}, {"source1": "./usr/share/doc/python-cogent-doc/html/cookbook/moltypes.html", "source2": "./usr/share/doc/python-cogent-doc/html/cookbook/moltypes.html", "unified_diff": "@@ -4,26 +4,26 @@\n \n \n \n \n \n \n \n- Molecular types — cogent3 2024.11.09 documentation\n+ Molecular types — cogent3 2025.12.14 documentation\n \n \n \n \n \n \n \n- \n+ \n \n \n \n \n \n \n \n"}, {"source1": "./usr/share/doc/python-cogent-doc/html/cookbook/protein_sequences.html", "source2": "./usr/share/doc/python-cogent-doc/html/cookbook/protein_sequences.html", "unified_diff": "@@ -4,26 +4,26 @@\n \n \n \n \n \n \n \n- Protein sequences — cogent3 2024.11.09 documentation\n+ Protein sequences — cogent3 2025.12.14 documentation\n \n \n \n \n \n \n \n- \n+ \n \n \n \n \n \n \n \n"}, {"source1": "./usr/share/doc/python-cogent-doc/html/cookbook/simple_trees.html", "source2": "./usr/share/doc/python-cogent-doc/html/cookbook/simple_trees.html", "unified_diff": "@@ -4,26 +4,26 @@\n \n \n \n \n \n \n \n- Trees — cogent3 2024.11.09 documentation\n+ Trees — cogent3 2025.12.14 documentation\n \n \n \n \n \n \n \n- \n+ \n \n \n \n \n \n \n \n"}, {"source1": "./usr/share/doc/python-cogent-doc/html/cookbook/tables.html", "source2": "./usr/share/doc/python-cogent-doc/html/cookbook/tables.html", "unified_diff": "@@ -4,26 +4,26 @@\n \n \n \n \n \n \n \n- Tabular data — cogent3 2024.11.09 documentation\n+ Tabular data — cogent3 2025.12.14 documentation\n \n \n \n \n \n \n \n- \n+ \n \n \n \n \n \n \n \n"}, {"source1": "./usr/share/doc/python-cogent-doc/html/cookbook/union_dict.html", "source2": "./usr/share/doc/python-cogent-doc/html/cookbook/union_dict.html", "unified_diff": "@@ -4,26 +4,26 @@\n \n \n \n \n \n \n \n- UnionDict \u2013 a dict with set like operations and keys as attributes — cogent3 2024.11.09 documentation\n+ UnionDict \u2013 a dict with set like operations and keys as attributes — cogent3 2025.12.14 documentation\n \n \n \n \n \n \n \n- \n+ \n \n \n \n \n \n \n \n"}, {"source1": "./usr/share/doc/python-cogent-doc/html/cookbook/useful_utilities.html", "source2": "./usr/share/doc/python-cogent-doc/html/cookbook/useful_utilities.html", "unified_diff": "@@ -4,26 +4,26 @@\n \n \n \n \n \n \n \n- Useful Utilities — cogent3 2024.11.09 documentation\n+ Useful Utilities — cogent3 2025.12.14 documentation\n \n \n \n \n \n \n \n- \n+ \n \n \n \n \n \n \n \n"}, {"source1": "./usr/share/doc/python-cogent-doc/html/cookbook/what_codes.html", "source2": "./usr/share/doc/python-cogent-doc/html/cookbook/what_codes.html", "unified_diff": "@@ -4,26 +4,26 @@\n \n \n \n \n \n \n \n- Available genetic codes — cogent3 2024.11.09 documentation\n+ Available genetic codes — cogent3 2025.12.14 documentation\n \n \n \n \n \n \n \n- \n+ \n \n \n \n \n \n \n \n"}, {"source1": "./usr/share/doc/python-cogent-doc/html/data_file_links.html", "source2": "./usr/share/doc/python-cogent-doc/html/data_file_links.html", "unified_diff": "@@ -4,26 +4,26 @@\n \n \n \n \n \n \n \n- Data Files Used in the Documentation — cogent3 2024.11.09 documentation\n+ Data Files Used in the Documentation — cogent3 2025.12.14 documentation\n \n \n \n \n \n \n \n- \n+ \n \n \n \n \n \n \n \n"}, {"source1": "./usr/share/doc/python-cogent-doc/html/draw/aln/plot_aln-coevolution.html", "source2": "./usr/share/doc/python-cogent-doc/html/draw/aln/plot_aln-coevolution.html", "unified_diff": "@@ -4,26 +4,26 @@\n \n \n \n \n \n \n \n- Coevolution analysis — cogent3 2024.11.09 documentation\n+ Coevolution analysis — cogent3 2025.12.14 documentation\n \n \n \n \n \n \n \n- \n+ \n \n \n \n \n \n \n \n"}, {"source1": "./usr/share/doc/python-cogent-doc/html/draw/aln/plot_aln-dotplot-1.html", "source2": "./usr/share/doc/python-cogent-doc/html/draw/aln/plot_aln-dotplot-1.html", "unified_diff": "@@ -4,26 +4,26 @@\n \n \n \n \n \n \n \n- Dotplot basics — cogent3 2024.11.09 documentation\n+ Dotplot basics — cogent3 2025.12.14 documentation\n \n \n \n \n \n \n \n- \n+ \n \n \n \n \n \n \n \n"}, {"source1": "./usr/share/doc/python-cogent-doc/html/draw/aln/plot_aln-dotplot-2.html", "source2": "./usr/share/doc/python-cogent-doc/html/draw/aln/plot_aln-dotplot-2.html", "unified_diff": "@@ -4,26 +4,26 @@\n \n \n \n \n \n \n \n- Dotplot with annotated sequences — cogent3 2024.11.09 documentation\n+ Dotplot with annotated sequences — cogent3 2025.12.14 documentation\n \n \n \n \n \n \n \n- \n+ \n \n \n \n \n \n \n \n"}, {"source1": "./usr/share/doc/python-cogent-doc/html/draw/aln/plot_aln-dotplot-3.html", "source2": "./usr/share/doc/python-cogent-doc/html/draw/aln/plot_aln-dotplot-3.html", "unified_diff": "@@ -4,26 +4,26 @@\n \n \n \n \n \n \n \n- Assess alignment quality via dotplots — cogent3 2024.11.09 documentation\n+ Assess alignment quality via dotplots — cogent3 2025.12.14 documentation\n \n \n \n \n \n \n \n- \n+ \n \n \n \n \n \n \n \n"}, {"source1": "./usr/share/doc/python-cogent-doc/html/draw/aln/plot_aln-gaps-per-seq.html", "source2": "./usr/share/doc/python-cogent-doc/html/draw/aln/plot_aln-gaps-per-seq.html", "unified_diff": "@@ -4,26 +4,26 @@\n \n \n \n \n \n \n \n- Counting gaps per sequence — cogent3 2024.11.09 documentation\n+ Counting gaps per sequence — cogent3 2025.12.14 documentation\n \n \n \n \n \n \n \n- \n+ \n \n \n \n \n \n \n \n"}, {"source1": "./usr/share/doc/python-cogent-doc/html/draw/aln/plot_aln-info-plot.html", "source2": "./usr/share/doc/python-cogent-doc/html/draw/aln/plot_aln-info-plot.html", "unified_diff": "@@ -4,26 +4,26 @@\n \n \n \n \n \n \n \n- Information analysis of an alignment — cogent3 2024.11.09 documentation\n+ Information analysis of an alignment — cogent3 2025.12.14 documentation\n \n \n \n \n \n \n \n- \n+ \n \n \n \n \n \n \n \n"}, {"source1": "./usr/share/doc/python-cogent-doc/html/draw/aln/plot_aln-seqlogo.html", "source2": "./usr/share/doc/python-cogent-doc/html/draw/aln/plot_aln-seqlogo.html", "unified_diff": "@@ -4,26 +4,26 @@\n \n \n \n \n \n \n \n- Sequence logos — cogent3 2024.11.09 documentation\n+ Sequence logos — cogent3 2025.12.14 documentation\n \n \n \n \n \n \n \n- \n+ \n \n \n \n \n \n \n \n"}, {"source1": "./usr/share/doc/python-cogent-doc/html/draw/aln/plot_seq-features.html", "source2": "./usr/share/doc/python-cogent-doc/html/draw/aln/plot_seq-features.html", "unified_diff": "@@ -4,26 +4,26 @@\n \n \n \n \n \n \n \n- Sequence Features — cogent3 2024.11.09 documentation\n+ Sequence Features — cogent3 2025.12.14 documentation\n \n \n \n \n \n \n \n- \n+ \n \n \n \n \n \n \n \n"}, {"source1": "./usr/share/doc/python-cogent-doc/html/draw/index.html", "source2": "./usr/share/doc/python-cogent-doc/html/draw/index.html", "unified_diff": "@@ -4,27 +4,27 @@\n \n \n \n \n \n \n \n- Image Gallery — cogent3 2024.11.09 documentation\n+ Image Gallery — cogent3 2025.12.14 documentation\n \n \n \n \n \n \n \n \n- \n+ \n \n \n \n \n \n \n \n"}, {"source1": "./usr/share/doc/python-cogent-doc/html/draw/tree/plot_tree-angular.html", "source2": "./usr/share/doc/python-cogent-doc/html/draw/tree/plot_tree-angular.html", "unified_diff": "@@ -4,26 +4,26 @@\n \n \n \n \n \n \n \n- Angular Dendrogram Style — cogent3 2024.11.09 documentation\n+ Angular Dendrogram Style — cogent3 2025.12.14 documentation\n \n \n \n \n \n \n \n- \n+ \n \n \n \n \n \n \n \n"}, {"source1": "./usr/share/doc/python-cogent-doc/html/draw/tree/plot_tree-circular.html", "source2": "./usr/share/doc/python-cogent-doc/html/draw/tree/plot_tree-circular.html", "unified_diff": "@@ -4,26 +4,26 @@\n \n \n \n \n \n \n \n- Circular Dendrogram Style — cogent3 2024.11.09 documentation\n+ Circular Dendrogram Style — cogent3 2025.12.14 documentation\n \n \n \n \n \n \n \n- \n+ \n \n \n \n \n \n \n \n"}, {"source1": "./usr/share/doc/python-cogent-doc/html/draw/tree/plot_tree-radial.html", "source2": "./usr/share/doc/python-cogent-doc/html/draw/tree/plot_tree-radial.html", "unified_diff": "@@ -4,26 +4,26 @@\n \n \n \n \n \n \n \n- Radial Dendrogram Style — cogent3 2024.11.09 documentation\n+ Radial Dendrogram Style — cogent3 2025.12.14 documentation\n \n \n \n \n \n \n \n- \n+ \n \n \n \n \n \n \n \n"}, {"source1": "./usr/share/doc/python-cogent-doc/html/draw/tree/plot_tree-square.html", "source2": "./usr/share/doc/python-cogent-doc/html/draw/tree/plot_tree-square.html", "unified_diff": "@@ -4,26 +4,26 @@\n \n \n \n \n \n \n \n- Square Dendrogram Style — cogent3 2024.11.09 documentation\n+ Square Dendrogram Style — cogent3 2025.12.14 documentation\n \n \n \n \n \n \n \n- \n+ \n \n \n \n \n \n \n \n"}, {"source1": "./usr/share/doc/python-cogent-doc/html/draw/tree/plot_tree-support.html", "source2": "./usr/share/doc/python-cogent-doc/html/draw/tree/plot_tree-support.html", "unified_diff": "@@ -4,26 +4,26 @@\n \n \n \n \n \n \n \n- Showing Bootstrap Support — cogent3 2024.11.09 documentation\n+ Showing Bootstrap Support — cogent3 2025.12.14 documentation\n \n \n \n \n \n \n \n- \n+ \n \n \n \n \n \n \n \n"}, {"source1": "./usr/share/doc/python-cogent-doc/html/examples/align_codons_to_protein.html", "source2": "./usr/share/doc/python-cogent-doc/html/examples/align_codons_to_protein.html", "unified_diff": "@@ -4,26 +4,26 @@\n \n \n \n \n \n \n \n- Map protein alignment gaps to DNA alignment gaps — cogent3 2024.11.09 documentation\n+ Map protein alignment gaps to DNA alignment gaps — cogent3 2025.12.14 documentation\n \n \n \n \n \n \n \n- \n+ \n \n \n \n \n \n \n \n"}, {"source1": "./usr/share/doc/python-cogent-doc/html/examples/calculate_UPGMA_cluster.html", "source2": "./usr/share/doc/python-cogent-doc/html/examples/calculate_UPGMA_cluster.html", "unified_diff": "@@ -4,26 +4,26 @@\n \n \n \n \n \n \n \n- Make a UPGMA cluster — cogent3 2024.11.09 documentation\n+ Make a UPGMA cluster — cogent3 2025.12.14 documentation\n \n \n \n \n \n \n \n- \n+ \n \n \n \n \n \n \n \n"}, {"source1": "./usr/share/doc/python-cogent-doc/html/examples/calculate_neigbourjoining_tree.html", "source2": "./usr/share/doc/python-cogent-doc/html/examples/calculate_neigbourjoining_tree.html", "unified_diff": "@@ -4,26 +4,26 @@\n \n \n \n \n \n \n \n- Make a neighbor joining tree — cogent3 2024.11.09 documentation\n+ Make a neighbor joining tree — cogent3 2025.12.14 documentation\n \n \n \n \n \n \n \n- \n+ \n \n \n \n \n \n \n \n"}, {"source1": "./usr/share/doc/python-cogent-doc/html/examples/calculate_pairwise_distances.html", "source2": "./usr/share/doc/python-cogent-doc/html/examples/calculate_pairwise_distances.html", "unified_diff": "@@ -4,26 +4,26 @@\n \n \n \n \n \n \n \n- Calculate pairwise distances between sequences — cogent3 2024.11.09 documentation\n+ Calculate pairwise distances between sequences — cogent3 2025.12.14 documentation\n \n \n \n \n \n \n \n- \n+ \n \n \n \n \n \n \n \n"}, {"source1": "./usr/share/doc/python-cogent-doc/html/examples/codon_models.html", "source2": "./usr/share/doc/python-cogent-doc/html/examples/codon_models.html", "unified_diff": "@@ -4,26 +4,26 @@\n \n \n \n \n \n \n \n- Using codon models — cogent3 2024.11.09 documentation\n+ Using codon models — cogent3 2025.12.14 documentation\n \n \n \n \n \n \n \n- \n+ \n \n \n \n \n \n \n \n"}, {"source1": "./usr/share/doc/python-cogent-doc/html/examples/coevolution.html", "source2": "./usr/share/doc/python-cogent-doc/html/examples/coevolution.html", "unified_diff": "@@ -4,26 +4,26 @@\n \n \n \n \n \n \n \n- Perform a coevolutionary analysis on biological sequence alignments — cogent3 2024.11.09 documentation\n+ Perform a coevolutionary analysis on biological sequence alignments — cogent3 2025.12.14 documentation\n \n \n \n \n \n \n \n- \n+ \n \n \n \n \n \n \n \n"}, {"source1": "./usr/share/doc/python-cogent-doc/html/examples/empirical_protein_models.html", "source2": "./usr/share/doc/python-cogent-doc/html/examples/empirical_protein_models.html", "unified_diff": "@@ -4,26 +4,26 @@\n \n \n \n \n \n \n \n- Use an empirical protein substitution model — cogent3 2024.11.09 documentation\n+ Use an empirical protein substitution model — cogent3 2025.12.14 documentation\n \n \n \n \n \n \n \n- \n+ \n \n \n \n \n \n \n \n"}, {"source1": "./usr/share/doc/python-cogent-doc/html/examples/hmm_par_heterogeneity.html", "source2": "./usr/share/doc/python-cogent-doc/html/examples/hmm_par_heterogeneity.html", "unified_diff": "@@ -4,26 +4,26 @@\n \n \n \n \n \n \n \n- Evaluate process heterogeneity using a Hidden Markov Model — cogent3 2024.11.09 documentation\n+ Evaluate process heterogeneity using a Hidden Markov Model — cogent3 2025.12.14 documentation\n \n \n \n \n \n \n \n- \n+ \n \n \n \n \n \n \n \n"}, {"source1": "./usr/share/doc/python-cogent-doc/html/examples/index.html", "source2": "./usr/share/doc/python-cogent-doc/html/examples/index.html", "unified_diff": "@@ -4,26 +4,26 @@\n \n \n \n \n \n \n \n- Tutorials — cogent3 2024.11.09 documentation\n+ Tutorials — cogent3 2025.12.14 documentation\n \n \n \n \n \n \n \n- \n+ \n \n \n \n \n \n \n \n"}, {"source1": "./usr/share/doc/python-cogent-doc/html/examples/manipulating_tree_nodes.html", "source2": "./usr/share/doc/python-cogent-doc/html/examples/manipulating_tree_nodes.html", "unified_diff": "@@ -4,26 +4,26 @@\n \n \n \n \n \n \n \n- Manipulation of Tree Node Objects — cogent3 2024.11.09 documentation\n+ Manipulation of Tree Node Objects — cogent3 2025.12.14 documentation\n \n \n \n \n \n \n \n- \n+ \n \n \n \n \n \n \n \n"}, {"source1": "./usr/share/doc/python-cogent-doc/html/examples/neutral_test.html", "source2": "./usr/share/doc/python-cogent-doc/html/examples/neutral_test.html", "unified_diff": "@@ -4,26 +4,26 @@\n \n \n \n \n \n \n \n- A test of the neutral theory — cogent3 2024.11.09 documentation\n+ A test of the neutral theory — cogent3 2025.12.14 documentation\n \n \n \n \n \n \n \n- \n+ \n \n \n \n \n \n \n \n"}, {"source1": "./usr/share/doc/python-cogent-doc/html/examples/parallel.html", "source2": "./usr/share/doc/python-cogent-doc/html/examples/parallel.html", "unified_diff": "@@ -4,26 +4,26 @@\n \n \n \n \n \n \n \n- Parallel computations — cogent3 2024.11.09 documentation\n+ Parallel computations — cogent3 2025.12.14 documentation\n \n \n \n \n \n \n \n- \n+ \n \n \n \n \n \n \n \n"}, {"source1": "./usr/share/doc/python-cogent-doc/html/examples/parametric_bootstrap.html", "source2": "./usr/share/doc/python-cogent-doc/html/examples/parametric_bootstrap.html", "unified_diff": "@@ -4,26 +4,26 @@\n \n \n \n \n \n \n \n- Performing a parametric bootstrap — cogent3 2024.11.09 documentation\n+ Performing a parametric bootstrap — cogent3 2025.12.14 documentation\n \n \n \n \n \n \n \n- \n+ \n \n \n \n \n \n \n \n"}, {"source1": "./usr/share/doc/python-cogent-doc/html/examples/period_estimation.html", "source2": "./usr/share/doc/python-cogent-doc/html/examples/period_estimation.html", "unified_diff": "@@ -4,26 +4,26 @@\n \n \n \n \n \n \n \n- Estimating periodic signals — cogent3 2024.11.09 documentation\n+ Estimating periodic signals — cogent3 2025.12.14 documentation\n \n \n \n \n \n \n \n- \n+ \n \n \n \n \n \n \n \n"}, {"source1": "./usr/share/doc/python-cogent-doc/html/examples/phylo_by_ls.html", "source2": "./usr/share/doc/python-cogent-doc/html/examples/phylo_by_ls.html", "unified_diff": "@@ -4,26 +4,26 @@\n \n \n \n \n \n \n \n- Phylogenetic reconstruction by least squares — cogent3 2024.11.09 documentation\n+ Phylogenetic reconstruction by least squares — cogent3 2025.12.14 documentation\n \n \n \n \n \n \n \n- \n+ \n \n \n \n \n \n \n \n"}, {"source1": "./usr/share/doc/python-cogent-doc/html/examples/rate_heterogeneity.html", "source2": "./usr/share/doc/python-cogent-doc/html/examples/rate_heterogeneity.html", "unified_diff": "@@ -4,26 +4,26 @@\n \n \n \n \n \n \n \n- Analysis of rate heterogeneity — cogent3 2024.11.09 documentation\n+ Analysis of rate heterogeneity — cogent3 2025.12.14 documentation\n \n \n \n \n \n \n \n- \n+ \n \n \n \n \n \n \n \n"}, {"source1": "./usr/share/doc/python-cogent-doc/html/examples/relative_rate.html", "source2": "./usr/share/doc/python-cogent-doc/html/examples/relative_rate.html", "unified_diff": "@@ -4,26 +4,26 @@\n \n \n \n \n \n \n \n- Performing a relative rate test — cogent3 2024.11.09 documentation\n+ Performing a relative rate test — cogent3 2025.12.14 documentation\n \n \n \n \n \n \n \n- \n+ \n \n \n \n \n \n \n \n"}, {"source1": "./usr/share/doc/python-cogent-doc/html/examples/scope_model_params_on_trees.html", "source2": "./usr/share/doc/python-cogent-doc/html/examples/scope_model_params_on_trees.html", "unified_diff": "@@ -4,26 +4,26 @@\n \n \n \n \n \n \n \n- Allowing substitution model parameters to differ between branches — cogent3 2024.11.09 documentation\n+ Allowing substitution model parameters to differ between branches — cogent3 2025.12.14 documentation\n \n \n \n \n \n \n \n- \n+ \n \n \n \n \n \n \n \n"}, {"source1": "./usr/share/doc/python-cogent-doc/html/examples/simple.html", "source2": "./usr/share/doc/python-cogent-doc/html/examples/simple.html", "unified_diff": "@@ -4,26 +4,26 @@\n \n \n \n \n \n \n \n- The simplest script — cogent3 2024.11.09 documentation\n+ The simplest script — cogent3 2025.12.14 documentation\n \n \n \n \n \n \n \n- \n+ \n \n \n \n \n \n \n \n"}, {"source1": "./usr/share/doc/python-cogent-doc/html/examples/simulate_alignment.html", "source2": "./usr/share/doc/python-cogent-doc/html/examples/simulate_alignment.html", "unified_diff": "@@ -4,26 +4,26 @@\n \n \n \n \n \n \n \n- Simulate an alignment — cogent3 2024.11.09 documentation\n+ Simulate an alignment — cogent3 2025.12.14 documentation\n \n \n \n \n \n \n \n- \n+ \n \n \n \n \n \n \n \n"}, {"source1": "./usr/share/doc/python-cogent-doc/html/examples/testing_multi_loci.html", "source2": "./usr/share/doc/python-cogent-doc/html/examples/testing_multi_loci.html", "unified_diff": "@@ -4,26 +4,26 @@\n \n \n \n \n \n \n \n- Likelihood analysis of multiple loci — cogent3 2024.11.09 documentation\n+ Likelihood analysis of multiple loci — cogent3 2025.12.14 documentation\n \n \n \n \n \n \n \n- \n+ \n \n \n \n \n \n \n \n"}, {"source1": "./usr/share/doc/python-cogent-doc/html/genindex.html", "source2": "./usr/share/doc/python-cogent-doc/html/genindex.html", "unified_diff": "@@ -3,26 +3,26 @@\n \n \n \n \n \n \n \n- Index — cogent3 2024.11.09 documentation\n+ Index — cogent3 2025.12.14 documentation\n \n \n \n \n \n \n \n- \n+ \n \n \n \n \n \n \n \n"}, {"source1": "./usr/share/doc/python-cogent-doc/html/index.html", "source2": "./usr/share/doc/python-cogent-doc/html/index.html", "unified_diff": "@@ -4,26 +4,26 @@\n \n \n \n \n \n \n \n- User Guides — cogent3 2024.11.09 documentation\n+ User Guides — cogent3 2025.12.14 documentation\n \n \n \n \n \n \n \n- \n+ \n \n \n \n \n \n \n \n"}, {"source1": "./usr/share/doc/python-cogent-doc/html/install.html", "source2": "./usr/share/doc/python-cogent-doc/html/install.html", "unified_diff": "@@ -4,26 +4,26 @@\n \n \n \n \n \n \n \n- Installation — cogent3 2024.11.09 documentation\n+ Installation — cogent3 2025.12.14 documentation\n \n \n \n \n \n \n \n- \n+ \n \n \n \n \n \n \n \n"}, {"source1": "./usr/share/doc/python-cogent-doc/html/licenses.html", "source2": "./usr/share/doc/python-cogent-doc/html/licenses.html", "unified_diff": "@@ -4,26 +4,26 @@\n \n \n \n \n \n \n \n- License — cogent3 2024.11.09 documentation\n+ License — cogent3 2025.12.14 documentation\n \n \n \n \n \n \n \n- \n+ \n \n \n \n \n \n \n \n"}, {"source1": "./usr/share/doc/python-cogent-doc/html/pycogent.html", "source2": "./usr/share/doc/python-cogent-doc/html/pycogent.html", "unified_diff": "@@ -4,26 +4,26 @@\n \n \n \n \n \n \n \n- How does cogent3 relate to PyCogent? — cogent3 2024.11.09 documentation\n+ How does cogent3 relate to PyCogent? — cogent3 2025.12.14 documentation\n \n \n \n \n \n \n \n- \n+ \n \n \n \n \n \n \n \n"}, {"source1": "./usr/share/doc/python-cogent-doc/html/search.html", "source2": "./usr/share/doc/python-cogent-doc/html/search.html", "unified_diff": "@@ -2,26 +2,26 @@\n \n \n \n \n \n \n \n- Search - cogent3 2024.11.09 documentation\n+ Search - cogent3 2025.12.14 documentation\n \n \n \n \n \n \n \n- \n+ \n \n \n \n \n \n \n \n"}, {"source1": "./usr/share/doc/python-cogent-doc/html/templates/class.html", "source2": "./usr/share/doc/python-cogent-doc/html/templates/class.html", "unified_diff": "@@ -4,26 +4,26 @@\n \n \n \n \n \n \n \n- <no title> — cogent3 2024.11.09 documentation\n+ <no title> — cogent3 2025.12.14 documentation\n \n \n \n \n \n \n \n- \n+ \n \n \n \n \n \n \n \n"}]}]}]}]}