rename project to 'wisp'

.github/workflows/python_package.yml

@@ -17,7 +17,7 @@ jobs:
         uses: mamba-org/setup-micromamba@v2
         with:
           environment-file: environment.yml
-          environment-name: sprite
+          environment-name: wisp
           create-args: >-
             python=${{ matrix.python-version }}
           init-shell: bash

.gitignore

@@ -1,7 +1,7 @@
 .DS_Store
 
 .git.broken
-src/sprite_mask/__pycache__/
+src/wisp_mask/__pycache__/
 __pycache__/
 *.py[cod]
 *.py.tmp.*

.readthedocs.yaml

@@ -1,4 +1,4 @@
-# Read the Docs configuration file for sprite.
+# Read the Docs configuration file for wisp.
 # See https://docs.readthedocs.io/en/stable/config-file/v2.html
 
 version: 2

README.md

@@ -1,31 +1,31 @@
-`sprite`<img src="https://raw.githubusercontent.com/samuk-lab/sprite/master/docs/images/sprite_logo.png" align="right" width="20%">
+`wisp`<img src="https://raw.githubusercontent.com/samuk-lab/wisp/master/docs/images/wisp_logo.png" align="right" width="20%">
 ====================
 
-`sprite` builds population count masks from BAM/CRAM alignments or all-sites VCFs. It is a companion tool for [pixy](https://github.com/ksamuk/pixy/), though it works equally well on its own.
+`wisp` builds population count masks from BAM/CRAM alignments or all-sites VCFs. It is a companion tool for [pixy](https://github.com/ksamuk/pixy/), though it works equally well on its own.
 
 Population count masks let you correctly compute the denominators of π, d<sub>xy</sub>, Watterson's θ, and Tajima's D when working from a variants-only VCF — callable sites are counted per population rather than collapsed into a single cohort-wide pass/fail.
 
-Sprite is inspired by [mop](https://github.com/RILAB/mop), [clam](https://github.com/cademirch/clam), and makes heavy use of [mosdepth](https://github.com/brentp/mosdepth).
+Wisp is inspired by [mop](https://github.com/RILAB/mop), [clam](https://github.com/cademirch/clam), and makes heavy use of [mosdepth](https://github.com/brentp/mosdepth).
 
-> **Note:** `sprite` is pre-release (alpha) and pending validation. It will be distributed on Bioconda as `sprite-mask` once stable.
+> **Note:** `wisp` is pre-release (alpha) and pending validation. It will be distributed on Bioconda as `wisp-mask` once stable.
 
 ## Installation
 
 ```bash
-mamba create -n sprite python=3.11 pip git -c conda-forge
-mamba activate sprite
+mamba create -n wisp python=3.11 pip git -c conda-forge
+mamba activate wisp
 mamba install -c conda-forge samtools bcftools htslib mosdepth
-python -m pip install "git+https://github.com/samuk-lab/sprite.git"
+python -m pip install "git+https://github.com/samuk-lab/wisp.git"
 ```
 
 ## Usage
 
 ### From BAM/CRAM alignments
 
-`sprite` runs [mosdepth](https://github.com/brentp/mosdepth) on each sample and collapses per-sample pass intervals into a population count mask:
+`wisp` runs [mosdepth](https://github.com/brentp/mosdepth) on each sample and collapses per-sample pass intervals into a population count mask:
 
 ```bash
-sprite from-alignments \
+wisp from-alignments \
   --samples samples.tsv \
   --variants-vcf variants.vcf.gz \
   --out results \
@@ -43,7 +43,7 @@ sample_2   popB        /path/sample_2.cram
 
 If BAM/CRAM read groups include sample names, they must match the corresponding `sample_id`.
 
-When `--variants-vcf` is provided, `sprite` uses the variants-only VCF to fill in omitted
+When `--variants-vcf` is provided, `wisp` uses the variants-only VCF to fill in omitted
 alignment thresholds: `--min-dp`/`--max-dp` from per-sample `FORMAT/DP` and `--min-mapq`
 from `INFO/MQ` when those fields are available. Manually supplied threshold flags take
 precedence. The same VCF is also scanned for indels, symbolic structural variants, breakends,
@@ -54,7 +54,7 @@ population.
 ### From an all-sites VCF
 
 ```bash
-sprite from-vcf \
+wisp from-vcf \
   --all-sites-vcf all_sites.vcf.gz \
   --popfile populations.tsv \
   --min-dp 10 \
@@ -73,19 +73,19 @@ sample_2   popB
 A few things to know about VCF mode:
 
 - Every sample in the population file must appear in the VCF. VCF samples absent from the population file are ignored (with a warning).
-- Records may carry any `FILTER` value — the input is assumed to have been filtered as desired before running `sprite`.
+- Records may carry any `FILTER` value — the input is assumed to have been filtered as desired before running `wisp`.
 - A sample passes a site when `FORMAT/DP >= --min-dp`, if supplied `FORMAT/DP <= --max-dp`, and, when `FORMAT/GT` is present, the genotype is not missing.
 - At duplicate `CHROM:POS` records, a sample passes a site if any duplicate passes the depth thresholds. Duplicates must be contiguous, as in a coordinate-sorted VCF.
 - By default, all record types are used (SNPs, indels, symbolic alleles, invariant sites). Pass `--snps-only` to exclude indel sites while retaining invariant sites.
 
 ## Output
 
-`sprite` writes two files to `--out`:
+`wisp` writes two files to `--out`:
 
 | File | Description |
 |---|---|
-| `sprite.bed.gz` | bgzip-compressed, tabix-indexed population count mask |
-| `sprite.bed.gz.tbi` | tabix index |
+| `wisp.bed.gz` | bgzip-compressed, tabix-indexed population count mask |
+| `wisp.bed.gz.tbi` | tabix index |
 
 Use `--output-prefix` to change the filename stem; `.bed.gz` is always appended.
 

docs/about.rst

@@ -1,9 +1,9 @@
 About
 *****
 
-``sprite`` creates population count masks for population genomic workflows.
+``wisp`` creates population count masks for population genomic workflows.
 Where a conventional depth mask gives a single cohort-wide pass/fail per
-site, ``sprite`` reports how many samples in each population clear the depth
+site, ``wisp`` reports how many samples in each population clear the depth
 threshold.
 
 Why population count masks?
@@ -29,13 +29,13 @@ Input modes
 BAM/CRAM mode
 -------------
 
-In alignment mode, ``sprite`` runs ``mosdepth`` once per sample using a
+In alignment mode, ``wisp`` runs ``mosdepth`` once per sample using a
 two-bin quantization: below threshold and at-or-above threshold. It extracts
 the passing intervals, optionally clips them to a mask BED, intersects all
 sample pass BEDs with ``bedtools multiinter``, and assembles them into a
 population count mask.
 
-An optional variants-only VCF can modify this alignment workflow. ``sprite``
+An optional variants-only VCF can modify this alignment workflow. ``wisp``
 can estimate omitted depth and mapping-quality thresholds from the VCF, and
 it subtracts indel, structural-variant, breakend, and multi-nucleotide
 polymorphism spans from every sample pass BED. Because the final BED is
@@ -45,7 +45,7 @@ zero passing samples in every population.
 All-sites VCF mode
 ------------------
 
-In VCF mode, ``sprite`` reads ``FORMAT/DP`` values directly from an all-sites
+In VCF mode, ``wisp`` reads ``FORMAT/DP`` values directly from an all-sites
 VCF. A sample passes a base when its DP value is greater than or equal to
 ``--min-dp`` and, if ``--max-dp`` is supplied, less than or equal to
 ``--max-dp``. When ``FORMAT/GT`` is present, the genotype must also be
@@ -57,6 +57,6 @@ coordinate-sorted VCF.
 Sparse output
 =============
 
-``sprite`` omits intervals where all population counts are zero. Consumers
+``wisp`` omits intervals where all population counts are zero. Consumers
 should treat missing intervals as zero passing samples per population, not as
 unknown or skipped.

docs/api.rst

@@ -1,29 +1,29 @@
 API Reference
 *************
 
-The public interface is the ``sprite`` command line tool, but these modules are
+The public interface is the ``wisp`` command line tool, but these modules are
 useful when reading or extending the implementation.
 
 Configuration
 =============
 
-.. automodule:: sprite_mask.config
+.. automodule:: wisp_mask.config
    :members:
 
 Workflow
 ========
 
-.. automodule:: sprite_mask.workflow
+.. automodule:: wisp_mask.workflow
    :members: run_workflow, workflow_output_paths
 
 Samples
 =======
 
-.. automodule:: sprite_mask.samples
+.. automodule:: wisp_mask.samples
    :members:
 
 Output summaries
 ================
 
-.. automodule:: sprite_mask.summaries
+.. automodule:: wisp_mask.summaries
    :members: summarize_population_count_bed

docs/arguments.rst

@@ -1,12 +1,12 @@
 Arguments
 *********
 
-All arguments are listed below. ``sprite --help`` shows the same information.
+All arguments are listed below. ``wisp --help`` shows the same information.
 
 Commands
 ========
 
-``sprite`` has two subcommands:
+``wisp`` has two subcommands:
 
 **from-alignments**
     Build a population count mask from BAM/CRAM files via ``mosdepth``.
@@ -26,7 +26,7 @@ Core arguments
     is supplied.
 
 **--out PATH**
-    Output directory for the final ``sprite.bed.gz`` and tabix index.
+    Output directory for the final ``wisp.bed.gz`` and tabix index.
 
 Input-specific arguments
 ========================
@@ -66,20 +66,20 @@ Shared optional arguments
     intervals are emitted.
 
 **--output-prefix TEXT**
-    Output filename stem within ``--out``. Defaults to ``sprite``,
-    producing ``sprite.bed.gz`` and ``sprite.bed.gz.tbi``. ``.bed.gz``
+    Output filename stem within ``--out``. Defaults to ``wisp``,
+    producing ``wisp.bed.gz`` and ``wisp.bed.gz.tbi``. ``.bed.gz``
     is always appended.
 
 **--keep-work**
     Keep intermediate files in the working directory. By default, work
     files are removed after a successful run.
 
 **--force**
-    Overwrite existing final outputs. Without this flag, ``sprite`` refuses
-    to replace ``sprite.bed.gz`` or ``sprite.bed.gz.tbi``.
+    Overwrite existing final outputs. Without this flag, ``wisp`` refuses
+    to replace ``wisp.bed.gz`` or ``wisp.bed.gz.tbi``.
 
 **--version**
-    Print the installed ``sprite`` version and exit.
+    Print the installed ``wisp`` version and exit.
 
 **--help**
     Print the full help message and exit.
@@ -125,7 +125,7 @@ BAM/CRAM mode:
 
 .. code-block:: console
 
-   sprite from-alignments \
+   wisp from-alignments \
      --samples tests/test_data/1000g_5sample_chr20_smoke/samples.tsv \
      --min-dp 10 \
      --variants-vcf validation/cohort.variants.vcf.gz \
@@ -140,7 +140,7 @@ All-sites VCF mode:
 
 .. code-block:: console
 
-   sprite from-vcf \
+   wisp from-vcf \
      --all-sites-vcf validation/cohort.all_sites.vcf.gz \
      --popfile validation/sample_populations.tsv \
      --min-dp 10 \

docs/changelog.rst

@@ -13,5 +13,5 @@ Highlights:
   depth/MAPQ thresholds and exclude indel, structural-variant, breakend, and
   multi-nucleotide polymorphism spans.
 * Build the same output from prefiltered all-sites VCF ``FORMAT/DP`` values.
-* Write bgzipped and tabix-indexed ``sprite.bed.gz`` output.
+* Write bgzipped and tabix-indexed ``wisp.bed.gz`` output.
 * Include JSON metadata and population column headers in the output BED.

docs/conf.py

@@ -14,9 +14,9 @@
 sys.path.insert(0, str(ROOT / "src"))
 
 
-project = "sprite"
-copyright = "2026, sprite contributors"
-author = "sprite contributors"
+project = "wisp"
+copyright = "2026, wisp contributors"
+author = "wisp contributors"
 
 with (ROOT / "pyproject.toml").open("rb") as handle:
     release = tomllib.load(handle)["project"]["version"]
@@ -42,27 +42,27 @@
 html_static_path = []
 html_title = f"{project} {release}"
 
-htmlhelp_basename = "spritedoc"
+htmlhelp_basename = "wispdoc"
 
 latex_documents = [
     (
         master_doc,
-        "sprite.tex",
-        "sprite Documentation",
+        "wisp.tex",
+        "wisp Documentation",
         author,
         "manual",
     ),
 ]
 
-man_pages = [(master_doc, "sprite", "sprite Documentation", [author], 1)]
+man_pages = [(master_doc, "wisp", "wisp Documentation", [author], 1)]
 
 texinfo_documents = [
     (
         master_doc,
-        "sprite",
-        "sprite Documentation",
+        "wisp",
+        "wisp Documentation",
         author,
-        "sprite",
+        "wisp",
         "Build sparse depth-threshold mask BEDs from cohort alignment data or all-sites VCFs.",
         "Miscellaneous",
     ),

docs/development.rst

@@ -7,7 +7,7 @@ Set up a development environment
 .. code-block:: console
 
    mamba env create -f environment.yml
-   conda activate sprite
+   conda activate wisp
    python -m pip install -e ".[dev,docs]"
 
 Run checks
@@ -38,15 +38,15 @@ Project layout
 
 .. code-block:: text
 
-   src/sprite_mask/     package source
+   src/wisp_mask/     package source
    tests/               unit and workflow tests
    tests/test_data/     small 1000 Genomes fixtures and download scripts
    docs/                Sphinx documentation
 
 Implementation overview
 =======================
 
-The public CLI is defined in ``sprite_mask.cli``. Parsed arguments are converted
+The public CLI is defined in ``wisp_mask.cli``. Parsed arguments are converted
 to ``RunConfig`` and passed to ``run_workflow``. The workflow validates the input
-mode, runs either the BAM/CRAM or VCF builder, writes ``sprite.bed.gz``,
+mode, runs either the BAM/CRAM or VCF builder, writes ``wisp.bed.gz``,
 and creates the tabix index.