mafutils 0.2.0__tar.gz → 0.2.1__tar.gz

{mafutils-0.2.0 → mafutils-0.2.1}/.gitignore

@@ -9,4 +9,7 @@ data/
 # Regenerable benchmark pipeline output.
 benchmarks/results/
 benchmarks/summary.html
-benchmarks/.snakemake/
+benchmarks/.snakemake/
+
+# Stray runtime log mafutils fetch writes to its output dir by default.
+maf_fetch.log

{mafutils-0.2.0 → mafutils-0.2.1}/DEVELOPMENT.md

@@ -1,5 +1,9 @@
 # mafutils Development Notes
 
+Internal implementation notes, gotchas, and maintainer workflows (testing,
+releasing) for developing `mafutils` itself — see [`README.md`](README.md)
+for user-facing installation/usage docs.
+
 - `tests/example.maf.scaffold.idx` is preserved as an older, headerless
   scaffold-index fixture for comparison — it deliberately sits at
   `example.maf`'s *default* scaffold-index path
@@ -155,6 +159,36 @@
   backward-seek risk entirely rather than relying on any per-region
   processing order.
 
+## Development setup
+
+From a source checkout, an editable install picks up code changes without
+reinstalling:
+
+```bash
+pip install -e .
+```
+
+Or run directly against the checkout without installing at all:
+
+```bash
+python -m mafutils --help
+```
+
+## Testing
+
+From inside this `mafutils/` directory:
+
+```bash
+pytest tests/
+```
+
+`tests/test_compression.py` covers cross-cutting compression behavior
+(bgzip/gzip detection, index headers, index auto-derivation, and the
+per-command parallel/sequential/fallback logic) across all three compression
+types. `tests/test_validate.py` covers index integrity (size/mtime/hash
+header fields, `mafutils validate`'s three-way verdict, and `--verify-hash`
+on `fetch`/`stats`/`gc`).
+
 ## Releasing to PyPI
 
 - Publishing is triggered by pushing a Git tag that matches `v*` (for example

{mafutils-0.2.0/mafutils.egg-info → mafutils-0.2.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: mafutils
-Version: 0.2.0
+Version: 0.2.1
 Summary: Utilities for indexing, fetching, and summarizing MAFs.
 Author: Gregg Thomas
 License: MIT License
@@ -50,7 +50,7 @@ It currently provides five commands:
 
 ## Disclaimer
 
-This project was developed with significant assistance from a large language model (GPT-5 / Codex).
+This project was developed with significant assistance from large language models (GPT-5 / Codex, Claude Sonnet).
 
 ## Third-Party Code
 
@@ -61,69 +61,62 @@ for full attribution and license text.
 
 ## Installation
 
-From this `mafutils/` directory:
-
 ```bash
-pip install -e .
+pip install mafutils
 ```
 
-If you are using the current shared workflow environment instead of a separate
-package environment, you can also run it directly with:
-
-```bash
-python -m mafutils --help
-```
+This installs the `mafutils` command.
 
 ## Quick Start
 
 Show top-level help:
 
 ```bash
-python -m mafutils --help
+mafutils --help
 ```
 
 Create block and scaffold indexes for a MAF (defaults to
 `input.maf.block.idx` / `input.maf.scaffold.idx` if output paths are omitted):
 
 ```bash
-python -m mafutils index input.maf
+mafutils index input.maf
 ```
 
 Fetch trimmed MAF regions from a BED file (index defaults to
 `input.maf.block.idx`):
 
 ```bash
-python -m mafutils fetch input.maf regions.bed -o outdir
+mafutils fetch input.maf regions.bed -o outdir
 ```
 
 Fetch FASTA output instead of MAF:
 
 ```bash
-python -m mafutils fetch input.maf regions.bed -o outdir -f -fh species-coords-id
+mafutils fetch input.maf regions.bed -o outdir -f -fh species-coords-id
 ```
 
 Extract full scaffolds using a scaffold index:
 
 ```bash
-python -m mafutils fetch input.maf scaffolds.bed -m scaffold -o outdir
+mafutils fetch input.maf scaffolds.bed -m scaffold -o outdir
 ```
 
 Summarize an indexed MAF:
 
 ```bash
-python -m mafutils stats input.maf -o summary/example
+mafutils stats input.maf -o summary/example
 ```
 
 Calculate per-species GC content:
 
 ```bash
-python -m mafutils gc input.maf -o summary/example
+mafutils gc input.maf -o summary/example
 ```
 
 Check whether an index is still trustworthy (see Index Integrity below):
 
 ```bash
-python -m mafutils validate input.maf
+mafutils validate input.maf
 ```
 
 ## Compression
@@ -139,13 +132,10 @@ python -m mafutils validate input.maf
 If you plan to use `--processes > 1` against compressed input, compress with
 `bgzip` rather than plain `gzip` to get real parallel speedup.
 
-**No extra dependency for bgzip:** BGZF support is provided by
-`mafutils/lib/bgzf.py`, vendored from [Biopython](https://biopython.org/)
-(see the notice at the top of that file and `THIRD_PARTY_LICENSES.md`) rather
-than by depending on the `biopython` package, which would otherwise pull in
-`numpy` for no other reason. This does mean upstream bug fixes to that file
-aren't picked up automatically — see `DEVELOPMENT.md` if you're debugging a
-bgzip-related issue.
+**No extra dependency for bgzip:** BGZF support is vendored in
+`mafutils/lib/bgzf.py` rather than depending on the `biopython` package —
+see `DEVELOPMENT.md` for why, and [`THIRD_PARTY_LICENSES.md`](THIRD_PARTY_LICENSES.md)
+for attribution.
 
 ## Index Integrity
 
@@ -184,7 +174,7 @@ For a "check once, trust thereafter" workflow instead of passing
 Create block and scaffold indexes for a MAF file.
 
 ```bash
-python -m mafutils index MAF_FILE [BLOCK_INDEX] [SCAFFOLD_INDEX]
+mafutils index MAF_FILE [BLOCK_INDEX] [SCAFFOLD_INDEX]
 ```
 
 Arguments:
@@ -200,7 +190,7 @@ Arguments:
 Fetch regions or scaffolds from a MAF using an existing index.
 
 ```bash
-python -m mafutils fetch [OPTIONS] MAF_FILE BED_FILE
+mafutils fetch [OPTIONS] MAF_FILE BED_FILE
 ```
 
 Arguments:
@@ -239,7 +229,7 @@ file) order, and decodes shared blocks only once even when regions overlap.
 Summarize an indexed MAF at overall, species, and block levels.
 
 ```bash
-python -m mafutils stats [OPTIONS] MAF_FILE [INDEX_FILE]
+mafutils stats [OPTIONS] MAF_FILE [INDEX_FILE]
 ```
 
 Arguments:
@@ -276,7 +266,7 @@ GC is computed as `(G+C) / (A+C+G+T)`, case-insensitive; gaps, `N`, and other
 ambiguity codes are excluded from both the numerator and denominator.
 
 ```bash
-python -m mafutils gc MAF_FILE [INDEX_FILE] [OPTIONS]
+mafutils gc MAF_FILE [INDEX_FILE] [OPTIONS]
 ```
 
 Arguments:
@@ -329,7 +319,7 @@ two indexes weren't built together (e.g. only one was rebuilt) and
 shouldn't be trusted as a matched pair.
 
 ```bash
-python -m mafutils validate MAF_FILE [INDEX_FILE]
+mafutils validate MAF_FILE [INDEX_FILE]
 ```
 
 Arguments:
@@ -349,23 +339,7 @@ verdict. Exit codes:
 | `1` | MISMATCH | A conclusive difference was found (compression, size, or hash against the MAF file; or the block and scaffold index headers disagree) — rebuild the index(es). |
 | `2` | UNVERIFIABLE | Nothing contradicts, but there's no stored hash to be fully sure (the index predates this feature), or the scaffold index is missing/headerless so the pair couldn't be cross-checked. |
 
-## Testing
-
-From inside this `mafutils/` directory:
-
-```bash
-pytest tests/
-```
-
-`tests/test_compression.py` covers cross-cutting compression behavior
-(bgzip/gzip detection, index headers, index auto-derivation, and the
-per-command parallel/sequential/fallback logic described above) across all
-three compression types. `tests/test_validate.py` covers index integrity
-(size/mtime/hash header fields, `mafutils validate`'s three-way verdict, and
-`--verify-hash` on `fetch`/`stats`/`gc`).
-
 ## Notes
 
-- `python -m mafutils ...` is the supported invocation from a source checkout.
-- The installed console entrypoint is `mafutils ...` once the package is
-  installed.
+For development setup (installing from a source checkout), running the test
+suite, and internal implementation notes, see [`DEVELOPMENT.md`](DEVELOPMENT.md).

{mafutils-0.2.0 → mafutils-0.2.1}/README.md

@@ -13,7 +13,7 @@ It currently provides five commands:
 
 ## Disclaimer
 
-This project was developed with significant assistance from a large language model (GPT-5 / Codex).
+This project was developed with significant assistance from large language models (GPT-5 / Codex, Claude Sonnet).
 
 ## Third-Party Code
 
@@ -24,69 +24,62 @@ for full attribution and license text.
 
 ## Installation
 
-From this `mafutils/` directory:
-
 ```bash
-pip install -e .
+pip install mafutils
 ```
 
-If you are using the current shared workflow environment instead of a separate
-package environment, you can also run it directly with:
-
-```bash
-python -m mafutils --help
-```
+This installs the `mafutils` command.
 
 ## Quick Start
 
 Show top-level help:
 
 ```bash
-python -m mafutils --help
+mafutils --help
 ```
 
 Create block and scaffold indexes for a MAF (defaults to
 `input.maf.block.idx` / `input.maf.scaffold.idx` if output paths are omitted):
 
 ```bash
-python -m mafutils index input.maf
+mafutils index input.maf
 ```
 
 Fetch trimmed MAF regions from a BED file (index defaults to
 `input.maf.block.idx`):
 
 ```bash
-python -m mafutils fetch input.maf regions.bed -o outdir
+mafutils fetch input.maf regions.bed -o outdir
 ```
 
 Fetch FASTA output instead of MAF:
 
 ```bash
-python -m mafutils fetch input.maf regions.bed -o outdir -f -fh species-coords-id
+mafutils fetch input.maf regions.bed -o outdir -f -fh species-coords-id
 ```
 
 Extract full scaffolds using a scaffold index:
 
 ```bash
-python -m mafutils fetch input.maf scaffolds.bed -m scaffold -o outdir
+mafutils fetch input.maf scaffolds.bed -m scaffold -o outdir
 ```
 
 Summarize an indexed MAF:
 
 ```bash
-python -m mafutils stats input.maf -o summary/example
+mafutils stats input.maf -o summary/example
 ```
 
 Calculate per-species GC content:
 
 ```bash
-python -m mafutils gc input.maf -o summary/example
+mafutils gc input.maf -o summary/example
 ```
 
 Check whether an index is still trustworthy (see Index Integrity below):
 
 ```bash
-python -m mafutils validate input.maf
+mafutils validate input.maf
 ```
 
 ## Compression
@@ -102,13 +95,10 @@ python -m mafutils validate input.maf
 If you plan to use `--processes > 1` against compressed input, compress with
 `bgzip` rather than plain `gzip` to get real parallel speedup.
 
-**No extra dependency for bgzip:** BGZF support is provided by
-`mafutils/lib/bgzf.py`, vendored from [Biopython](https://biopython.org/)
-(see the notice at the top of that file and `THIRD_PARTY_LICENSES.md`) rather
-than by depending on the `biopython` package, which would otherwise pull in
-`numpy` for no other reason. This does mean upstream bug fixes to that file
-aren't picked up automatically — see `DEVELOPMENT.md` if you're debugging a
-bgzip-related issue.
+**No extra dependency for bgzip:** BGZF support is vendored in
+`mafutils/lib/bgzf.py` rather than depending on the `biopython` package —
+see `DEVELOPMENT.md` for why, and [`THIRD_PARTY_LICENSES.md`](THIRD_PARTY_LICENSES.md)
+for attribution.
 
 ## Index Integrity
 
@@ -147,7 +137,7 @@ For a "check once, trust thereafter" workflow instead of passing
 Create block and scaffold indexes for a MAF file.
 
 ```bash
-python -m mafutils index MAF_FILE [BLOCK_INDEX] [SCAFFOLD_INDEX]
+mafutils index MAF_FILE [BLOCK_INDEX] [SCAFFOLD_INDEX]
 ```
 
 Arguments:
@@ -163,7 +153,7 @@ Arguments:
 Fetch regions or scaffolds from a MAF using an existing index.
 
 ```bash
-python -m mafutils fetch [OPTIONS] MAF_FILE BED_FILE
+mafutils fetch [OPTIONS] MAF_FILE BED_FILE
 ```
 
 Arguments:
@@ -202,7 +192,7 @@ file) order, and decodes shared blocks only once even when regions overlap.
 Summarize an indexed MAF at overall, species, and block levels.
 
 ```bash
-python -m mafutils stats [OPTIONS] MAF_FILE [INDEX_FILE]
+mafutils stats [OPTIONS] MAF_FILE [INDEX_FILE]
 ```
 
 Arguments:
@@ -239,7 +229,7 @@ GC is computed as `(G+C) / (A+C+G+T)`, case-insensitive; gaps, `N`, and other
 ambiguity codes are excluded from both the numerator and denominator.
 
 ```bash
-python -m mafutils gc MAF_FILE [INDEX_FILE] [OPTIONS]
+mafutils gc MAF_FILE [INDEX_FILE] [OPTIONS]
 ```
 
 Arguments:
@@ -292,7 +282,7 @@ two indexes weren't built together (e.g. only one was rebuilt) and
 shouldn't be trusted as a matched pair.
 
 ```bash
-python -m mafutils validate MAF_FILE [INDEX_FILE]
+mafutils validate MAF_FILE [INDEX_FILE]
 ```
 
 Arguments:
@@ -312,23 +302,7 @@ verdict. Exit codes:
 | `1` | MISMATCH | A conclusive difference was found (compression, size, or hash against the MAF file; or the block and scaffold index headers disagree) — rebuild the index(es). |
 | `2` | UNVERIFIABLE | Nothing contradicts, but there's no stored hash to be fully sure (the index predates this feature), or the scaffold index is missing/headerless so the pair couldn't be cross-checked. |
 
-## Testing
-
-From inside this `mafutils/` directory:
-
-```bash
-pytest tests/
-```
-
-`tests/test_compression.py` covers cross-cutting compression behavior
-(bgzip/gzip detection, index headers, index auto-derivation, and the
-per-command parallel/sequential/fallback logic described above) across all
-three compression types. `tests/test_validate.py` covers index integrity
-(size/mtime/hash header fields, `mafutils validate`'s three-way verdict, and
-`--verify-hash` on `fetch`/`stats`/`gc`).
-
 ## Notes
 
-- `python -m mafutils ...` is the supported invocation from a source checkout.
-- The installed console entrypoint is `mafutils ...` once the package is
-  installed.
+For development setup (installing from a source checkout), running the test
+suite, and internal implementation notes, see [`DEVELOPMENT.md`](DEVELOPMENT.md).

{mafutils-0.2.0 → mafutils-0.2.1}/mafutils/_version.py

@@ -18,7 +18,7 @@ version_tuple: tuple[int | str, ...]
 commit_id: str | None
 __commit_id__: str | None
 
-__version__ = version = '0.2.0'
-__version_tuple__ = version_tuple = (0, 2, 0)
+__version__ = version = '0.2.1'
+__version_tuple__ = version_tuple = (0, 2, 1)
 
-__commit_id__ = commit_id = 'g5d2163b7c'
+__commit_id__ = commit_id = 'g5c611ce9e'

{mafutils-0.2.0 → mafutils-0.2.1}/mafutils/fetch.py

@@ -1075,8 +1075,15 @@ def fetchScaffoldsSequential(ordered_scaffolds, index, maf_file, maf_header, maf
 
 def run_fetch(args, cmdline="mafutils fetch"):
 
+    if not args.single_output:
+        os.makedirs(args.output, exist_ok=True);
+    # Create the output directory before deciding where the log goes -- the
+    # log path check below needs args.output to already exist, since that's
+    # the whole point of checking os.path.isdir() rather than just always
+    # joining onto it.
+
     logfilename = os.path.join(args.output, "maf_fetch.log") if os.path.isdir(args.output) else "maf_fetch.log"
-    maf_fetch_logger = LOGINIT.configureLogging(log_level="INFO", log_verbosity="BOTH", log_filename=logfilename, logger_name="maf_fetch_logger")
+    maf_fetch_logger = LOGINIT.configureLogging(log_level="INFO", log_verbosity="BOTH", log_filename=logfilename, logger_name="maf_fetch_logger", overwrite_log_file=True)
     LOG = logging.getLogger(maf_fetch_logger)
     # Set up logging
 
@@ -1105,9 +1112,6 @@ def run_fetch(args, cmdline="mafutils fetch"):
     if maf_compression not in ("none", "gz", "bgzip"):
         LOG.error(f"Unsupported MAF compression: {maf_compression}")
         sys.exit(1)
-    if not args.single_output:
-        os.makedirs(args.output, exist_ok=True);
-    # Create output directory if it doesn't exist
 
     index_file = args.index_file
     if index_file is None:

{mafutils-0.2.0 → mafutils-0.2.1/mafutils.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: mafutils
-Version: 0.2.0
+Version: 0.2.1
 Summary: Utilities for indexing, fetching, and summarizing MAFs.
 Author: Gregg Thomas
 License: MIT License
@@ -50,7 +50,7 @@ It currently provides five commands:
 
 ## Disclaimer
 
-This project was developed with significant assistance from a large language model (GPT-5 / Codex).
+This project was developed with significant assistance from large language models (GPT-5 / Codex, Claude Sonnet).
 
 ## Third-Party Code
 
@@ -61,69 +61,62 @@ for full attribution and license text.
 
 ## Installation
 
-From this `mafutils/` directory:
-
 ```bash
-pip install -e .
+pip install mafutils
 ```
 
-If you are using the current shared workflow environment instead of a separate
-package environment, you can also run it directly with:
-
-```bash
-python -m mafutils --help
-```
+This installs the `mafutils` command.
 
 ## Quick Start
 
 Show top-level help:
 
 ```bash
-python -m mafutils --help
+mafutils --help
 ```
 
 Create block and scaffold indexes for a MAF (defaults to
 `input.maf.block.idx` / `input.maf.scaffold.idx` if output paths are omitted):
 
 ```bash
-python -m mafutils index input.maf
+mafutils index input.maf
 ```
 
 Fetch trimmed MAF regions from a BED file (index defaults to
 `input.maf.block.idx`):
 
 ```bash
-python -m mafutils fetch input.maf regions.bed -o outdir
+mafutils fetch input.maf regions.bed -o outdir
 ```
 
 Fetch FASTA output instead of MAF:
 
 ```bash
-python -m mafutils fetch input.maf regions.bed -o outdir -f -fh species-coords-id
+mafutils fetch input.maf regions.bed -o outdir -f -fh species-coords-id
 ```
 
 Extract full scaffolds using a scaffold index:
 
 ```bash
-python -m mafutils fetch input.maf scaffolds.bed -m scaffold -o outdir
+mafutils fetch input.maf scaffolds.bed -m scaffold -o outdir
 ```
 
 Summarize an indexed MAF:
 
 ```bash
-python -m mafutils stats input.maf -o summary/example
+mafutils stats input.maf -o summary/example
 ```
 
 Calculate per-species GC content:
 
 ```bash
-python -m mafutils gc input.maf -o summary/example
+mafutils gc input.maf -o summary/example
 ```
 
 Check whether an index is still trustworthy (see Index Integrity below):
 
 ```bash
-python -m mafutils validate input.maf
+mafutils validate input.maf
 ```
 
 ## Compression
@@ -139,13 +132,10 @@ python -m mafutils validate input.maf
 If you plan to use `--processes > 1` against compressed input, compress with
 `bgzip` rather than plain `gzip` to get real parallel speedup.
 
-**No extra dependency for bgzip:** BGZF support is provided by
-`mafutils/lib/bgzf.py`, vendored from [Biopython](https://biopython.org/)
-(see the notice at the top of that file and `THIRD_PARTY_LICENSES.md`) rather
-than by depending on the `biopython` package, which would otherwise pull in
-`numpy` for no other reason. This does mean upstream bug fixes to that file
-aren't picked up automatically — see `DEVELOPMENT.md` if you're debugging a
-bgzip-related issue.
+**No extra dependency for bgzip:** BGZF support is vendored in
+`mafutils/lib/bgzf.py` rather than depending on the `biopython` package —
+see `DEVELOPMENT.md` for why, and [`THIRD_PARTY_LICENSES.md`](THIRD_PARTY_LICENSES.md)
+for attribution.
 
 ## Index Integrity
 
@@ -184,7 +174,7 @@ For a "check once, trust thereafter" workflow instead of passing
 Create block and scaffold indexes for a MAF file.
 
 ```bash
-python -m mafutils index MAF_FILE [BLOCK_INDEX] [SCAFFOLD_INDEX]
+mafutils index MAF_FILE [BLOCK_INDEX] [SCAFFOLD_INDEX]
 ```
 
 Arguments:
@@ -200,7 +190,7 @@ Arguments:
 Fetch regions or scaffolds from a MAF using an existing index.
 
 ```bash
-python -m mafutils fetch [OPTIONS] MAF_FILE BED_FILE
+mafutils fetch [OPTIONS] MAF_FILE BED_FILE
 ```
 
 Arguments:
@@ -239,7 +229,7 @@ file) order, and decodes shared blocks only once even when regions overlap.
 Summarize an indexed MAF at overall, species, and block levels.
 
 ```bash
-python -m mafutils stats [OPTIONS] MAF_FILE [INDEX_FILE]
+mafutils stats [OPTIONS] MAF_FILE [INDEX_FILE]
 ```
 
 Arguments:
@@ -276,7 +266,7 @@ GC is computed as `(G+C) / (A+C+G+T)`, case-insensitive; gaps, `N`, and other
 ambiguity codes are excluded from both the numerator and denominator.
 
 ```bash
-python -m mafutils gc MAF_FILE [INDEX_FILE] [OPTIONS]
+mafutils gc MAF_FILE [INDEX_FILE] [OPTIONS]
 ```
 
 Arguments:
@@ -329,7 +319,7 @@ two indexes weren't built together (e.g. only one was rebuilt) and
 shouldn't be trusted as a matched pair.
 
 ```bash
-python -m mafutils validate MAF_FILE [INDEX_FILE]
+mafutils validate MAF_FILE [INDEX_FILE]
 ```
 
 Arguments:
@@ -349,23 +339,7 @@ verdict. Exit codes:
 | `1` | MISMATCH | A conclusive difference was found (compression, size, or hash against the MAF file; or the block and scaffold index headers disagree) — rebuild the index(es). |
 | `2` | UNVERIFIABLE | Nothing contradicts, but there's no stored hash to be fully sure (the index predates this feature), or the scaffold index is missing/headerless so the pair couldn't be cross-checked. |
 
-## Testing
-
-From inside this `mafutils/` directory:
-
-```bash
-pytest tests/
-```
-
-`tests/test_compression.py` covers cross-cutting compression behavior
-(bgzip/gzip detection, index headers, index auto-derivation, and the
-per-command parallel/sequential/fallback logic described above) across all
-three compression types. `tests/test_validate.py` covers index integrity
-(size/mtime/hash header fields, `mafutils validate`'s three-way verdict, and
-`--verify-hash` on `fetch`/`stats`/`gc`).
-
 ## Notes
 
-- `python -m mafutils ...` is the supported invocation from a source checkout.
-- The installed console entrypoint is `mafutils ...` once the package is
-  installed.
+For development setup (installing from a source checkout), running the test
+suite, and internal implementation notes, see [`DEVELOPMENT.md`](DEVELOPMENT.md).

{mafutils-0.2.0 → mafutils-0.2.1}/mafutils.egg-info/SOURCES.txt

@@ -5,7 +5,6 @@ DEVELOPMENT.md
 LICENSE
 README.md
 THIRD_PARTY_LICENSES.md
-maf_fetch.log
 pyproject.toml
 .github/workflows/publish-pypi.yml
 benchmarks/README.md
@@ -13,7 +12,6 @@ benchmarks/Snakefile
 benchmarks/baseline-manual-timings.txt
 benchmarks/config.yaml
 benchmarks/history.csv
-benchmarks/maf_fetch.log
 benchmarks/notebook.ipynb
 benchmarks/parse_benchmarks.py
 benchmarks/rulegraph.png

{mafutils-0.2.0 → mafutils-0.2.1}/mafutils.egg-info/scm_file_list.json

@@ -4,7 +4,6 @@
     "README.md",
     ".codex",
     "DEVELOPMENT.md",
-    "maf_fetch.log",
     "pyproject.toml",
     "THIRD_PARTY_LICENSES.md",
     "LICENSE",
@@ -15,7 +14,6 @@
     "benchmarks/baseline-manual-timings.txt",
     "benchmarks/rulegraph.png",
     "benchmarks/parse_benchmarks.py",
-    "benchmarks/maf_fetch.log",
     "benchmarks/notebook.ipynb",
     "benchmarks/config.yaml",
     "benchmarks/profiles/slurm/config.yaml",

mafutils-0.2.1/mafutils.egg-info/scm_version.json

@@ -0,0 +1,8 @@
+{
+  "tag": "0.2.1",
+  "distance": 0,
+  "node": "g5c611ce9e5d735e4f0eec333e1c8b906eb815005",
+  "dirty": false,
+  "branch": "HEAD",
+  "node_date": "2026-07-21"
+}