orfdata 0.40.0__tar.gz → 0.42.0__tar.gz

{orfdata-0.40.0/orfdata.egg-info → orfdata-0.42.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: orfdata
-Version: 0.40.0
+Version: 0.42.0
 Summary: Reference proteomes with evidence-backed noncanonical ORFs on PyEnsembl genomes
 Author: OpenVax
 License-Expression: Apache-2.0
@@ -10,29 +10,21 @@ License-File: LICENSE
 Requires-Dist: datacache<2,>=1.29.3
 Requires-Dist: pandas<4,>=3
 Requires-Dist: pyyaml<7,>=6
-Provides-Extra: pyensembl
-Requires-Dist: pyensembl>=2.27.2; extra == "pyensembl"
-Provides-Extra: build-data
-Requires-Dist: openpyxl>=3.1; extra == "build-data"
+Requires-Dist: pyensembl>=2.27.2
+Requires-Dist: openpyxl<4,>=3.1
+Requires-Dist: pyarrow>=14
+Requires-Dist: biotite<3,>=1.6
+Requires-Dist: pyahocorasick<3,>=2.3
 Provides-Extra: canine-extraction
 Requires-Dist: apsw<4,>=3.54; extra == "canine-extraction"
-Requires-Dist: pyahocorasick<3,>=2.3; extra == "canine-extraction"
-Provides-Extra: viral
-Provides-Extra: data
-Requires-Dist: datacache<2,>=1.29.3; extra == "data"
-Provides-Extra: columnar
-Requires-Dist: pyarrow>=14; extra == "columnar"
 Provides-Extra: dev
 Requires-Dist: pytest; extra == "dev"
 Requires-Dist: ruff; extra == "dev"
 Requires-Dist: build; extra == "dev"
 Requires-Dist: twine; extra == "dev"
-Requires-Dist: openpyxl>=3.1; extra == "dev"
-Requires-Dist: pyensembl>=2.27.2; extra == "dev"
-Requires-Dist: datacache<2,>=1.29.3; extra == "dev"
 Requires-Dist: gb-io<0.5,>=0.4; extra == "dev"
 Requires-Dist: apsw<4,>=3.54; extra == "dev"
-Requires-Dist: pyahocorasick<3,>=2.3; extra == "dev"
+Requires-Dist: biopython<2,>=1.88; extra == "dev"
 Provides-Extra: docs
 Requires-Dist: mkdocs<2,>=1.6; extra == "docs"
 Requires-Dist: mkdocs-material<10,>=9.5; extra == "docs"
@@ -56,19 +48,34 @@ evidence.
 Use Python 3.11 or later. Install orfdata and one PyEnsembl annotation:
 
 ```sh
-python -m pip install 'orfdata[pyensembl,build-data]'
+python -m pip install 'orfdata'
 pyensembl install --release 115 --species human
 # For the ncORF evidence presets and "all":
 orfdata setup --species human --catalogs all
 ```
 
+The normal installation includes PyEnsembl, spreadsheet source readers, PyArrow
+exports and Biotite alignment support. Reference and measurement data are still
+downloaded explicitly and checked against their pinned checksums. The
+`canine-extraction` extra adds APSW only for extracting the original vendor
+database through its custom VFS; released dataset queries and rebuilds from
+normalized sources do not need it.
+
 List every bundled, downloadable or buildable resource and what is installed:
 
 ```sh
-orfdata download list
-orfdata download status
+orfdata data list
+orfdata data status
+orfdata data info pfizer-atlas-dog-peptide-evidence
+orfdata data fetch pfizer-atlas-dog-peptide-evidence
+orfdata data path pfizer-atlas-dog-peptide-evidence
 ```
 
+`data fetch NAME` downloads a published artifact or builds from pinned sources
+when no artifact is distributed. The same command handles optional catalogues
+such as `openprot-mouse` and datasets such as `peptideatlas-dog-peptides`.
+`downloads` and `download` are aliases for `data`; `info` and `path` stay offline.
+
 `orfdata setup --species human` also installs `gdc-viruses`, the default
 200-reference GDC viral screen for human transcriptome analysis;
 `--collections none` skips it. Viral support is part of the base install, and
@@ -143,7 +150,7 @@ immunopeptidomics: peptides eluted from HLA molecules.
 | Dog | none: no public dog Ribo-seq or ncORF MS exists | |
 
 Human's bundled catalogue needs no setup. For the others, `pip install
-"orfdata[data,build-data]"`, then `orfdata setup --species mouse` (or
+"orfdata"`, then `orfdata setup --species mouse` (or
 `zebrafish`, `worm`, `yeast`, or `human --catalogs all`) builds the catalogues
 from their sources' own files ([details](https://openvax.github.io/orfdata/catalogs/)).
 After `orfdata chains download` (add
@@ -216,11 +223,10 @@ Promoting further source records into the curated
 ## Measurement datasets
 
 RNA, ribosome and protein measurements are separate, downloadable datasets with
-the same species-scoped API. Install the `data` extra, then download and query
-one:
+the same species-scoped API. Download and query one explicitly:
 
 ```sh
-pip install 'orfdata[data]'
+pip install 'orfdata'
 orfdata datasets list
 orfdata datasets download ingolia-yeast-rna-ribo
 ```

{orfdata-0.40.0 → orfdata-0.42.0}/README.md

@@ -16,19 +16,34 @@ evidence.
 Use Python 3.11 or later. Install orfdata and one PyEnsembl annotation:
 
 ```sh
-python -m pip install 'orfdata[pyensembl,build-data]'
+python -m pip install 'orfdata'
 pyensembl install --release 115 --species human
 # For the ncORF evidence presets and "all":
 orfdata setup --species human --catalogs all
 ```
 
+The normal installation includes PyEnsembl, spreadsheet source readers, PyArrow
+exports and Biotite alignment support. Reference and measurement data are still
+downloaded explicitly and checked against their pinned checksums. The
+`canine-extraction` extra adds APSW only for extracting the original vendor
+database through its custom VFS; released dataset queries and rebuilds from
+normalized sources do not need it.
+
 List every bundled, downloadable or buildable resource and what is installed:
 
 ```sh
-orfdata download list
-orfdata download status
+orfdata data list
+orfdata data status
+orfdata data info pfizer-atlas-dog-peptide-evidence
+orfdata data fetch pfizer-atlas-dog-peptide-evidence
+orfdata data path pfizer-atlas-dog-peptide-evidence
 ```
 
+`data fetch NAME` downloads a published artifact or builds from pinned sources
+when no artifact is distributed. The same command handles optional catalogues
+such as `openprot-mouse` and datasets such as `peptideatlas-dog-peptides`.
+`downloads` and `download` are aliases for `data`; `info` and `path` stay offline.
+
 `orfdata setup --species human` also installs `gdc-viruses`, the default
 200-reference GDC viral screen for human transcriptome analysis;
 `--collections none` skips it. Viral support is part of the base install, and
@@ -103,7 +118,7 @@ immunopeptidomics: peptides eluted from HLA molecules.
 | Dog | none: no public dog Ribo-seq or ncORF MS exists | |
 
 Human's bundled catalogue needs no setup. For the others, `pip install
-"orfdata[data,build-data]"`, then `orfdata setup --species mouse` (or
+"orfdata"`, then `orfdata setup --species mouse` (or
 `zebrafish`, `worm`, `yeast`, or `human --catalogs all`) builds the catalogues
 from their sources' own files ([details](https://openvax.github.io/orfdata/catalogs/)).
 After `orfdata chains download` (add
@@ -176,11 +191,10 @@ Promoting further source records into the curated
 ## Measurement datasets
 
 RNA, ribosome and protein measurements are separate, downloadable datasets with
-the same species-scoped API. Install the `data` extra, then download and query
-one:
+the same species-scoped API. Download and query one explicitly:
 
 ```sh
-pip install 'orfdata[data]'
+pip install 'orfdata'
 orfdata datasets list
 orfdata datasets download ingolia-yeast-rna-ribo
 ```

{orfdata-0.40.0 → orfdata-0.42.0}/docs/catalogs.md

@@ -77,7 +77,7 @@ existing standalone local-file workflow.
 ## Mouse
 
 ```sh
-pip install "orfdata[data,build-data]"
+pip install "orfdata"
 orfdata setup --species mouse --accept-terms   # Three catalogues and the chains; about 130 MB of sources
 ```
 
@@ -116,8 +116,7 @@ ATG, CTG, GTG or TTG. Its types are uORF (8,294), lncORF (3,576), uoORF
 (1,950), iORF (1,749), dORF (741) and doORF (174).
 
 - **Sources.** The authors' BED and protein FASTA (MIT, pinned commit), the
-  paper's Table S3 (CC BY 4.0) and Ensembl 107's GTF; about 40 MB. Building
-  needs `orfdata[build-data]` for the spreadsheet.
+  paper's Table S3 (CC BY 4.0) and Ensembl 107's GTF; about 40 MB.
 - **Coding paths.** The BED garbles multi-exon block sizes, so each ORF's
   path comes from its representative transcript and transcript coordinates
   in Ensembl 107, checked against its genomic start, stop, BED span and
@@ -163,8 +162,7 @@ floor, remains available explicitly as `--version 1`.
   51,881 place on Ensembl 115.
 - **Sources.** Supplementary Data 3 (CC BY 4.0) and Ensembl 107's GTF, cDNA
   and ncRNA FASTAs; about 115 MB, of which the 32 MB GTF is the one Chang et
-  al.'s catalogue uses, so `orfdata setup` downloads it once. Building needs
-  `orfdata[build-data]`.
+  al.'s catalogue uses, so `orfdata setup` downloads it once.
 - **Evidence.** Presence in the source's set is aggregate Ribo-seq support:
   `RiboSeq()` selects every ORF, `RiboSeq(min_studies=2)` none.
 - **Length policy.** `catalog.query(min_protein_length=5)` and
@@ -430,7 +428,7 @@ silently dropped.
 
 PyEnsembl's `EnsemblRelease` has no T2T-CHM13 annotation, so orfdata pins
 Ensembl's rapid-release one (2022_07) and installs it on request, checking each
-file's size and SHA-256 (it needs `orfdata[pyensembl]`). The T2T Consortium's
+file's size and SHA-256. The T2T Consortium's
 GRCh38-to-CHM13 chain is public domain (CC0):
 
 ```sh
@@ -481,8 +479,7 @@ orfdata lift --species human --to GRCh37 --output orfs-grch37.json.gz
 error. `--catalog FILE` lifts a local catalogue instead, and `--chain FILE` uses
 your own chain file instead of a downloaded pin. Pass the result back with
 `--nc-orf-sources` for `orfdata proteome`; JSON and TSV exports include
-each record's original and the chain. Downloading chains needs the
-`orfdata[data]` extra, which adds DataCache. In Python:
+each record's original and the chain. In Python:
 
 ```python
 from orfdata import download_chain, lift_catalog, load_catalog, load_chain

{orfdata-0.40.0 → orfdata-0.42.0}/docs/copy-yeast.md

@@ -7,7 +7,7 @@ grown in glucose-limited chemostats. The strain is EUROSCARF Y11335 BY4742,
 with the reported genotype retained on each sample.
 
 ```sh
-pip install 'orfdata[data]'
+pip install 'orfdata'
 orfdata datasets info copy-yeast-abundance
 orfdata datasets download copy-yeast-abundance
 orfdata datasets pairs copy-yeast-abundance --basis condition_aggregate
@@ -101,7 +101,7 @@ between species, and different cultures/calibrations remain different experiment
 See [pairing and orthology](pairing.md).
 
 To rebuild the release from the pinned public workbook, standards, metadata and
-four RNA files, install `orfdata[data,build-data]` and run
+four RNA files, install `orfdata` and run
 `orfdata datasets build copy-yeast-abundance`. Python uses
 `DatasetRegistry().build("copy-yeast-abundance")`. Local verified inputs can be
 supplied with repeated `--source-path ASSET=PATH` or `source_paths={...}`.

orfdata-0.42.0/docs/dog-data-sources.md

@@ -0,0 +1,60 @@
+# Canine paired measurements and translation-evidence audit
+
+Source check: **28 October 2026**. This audit identifies importable measurement
+files and their limitations. It does not add a dataset to the registry.
+The [machine-readable audit](data/dog-source-audit-20261028.json) contains source
+URLs, hashes, counts, search queries and a candidate sample crosswalk.
+
+## Paired RNA and protein: a verified study
+
+[Amini et al., 2021](https://pmc.ncbi.nlm.nih.gov/articles/PMC8042244/)
+studied cancer-associated and normal stroma from archived canine mammary
+carcinomas. The authors explicitly reused the cases of their earlier RNA study.
+Original case 7 was excluded from proteomics because its paraffin block was
+unavailable. Measurements come from separate laser-capture preparations of
+the same tissue cases, not identical RNA/protein aliquots.
+
+| Source | Verified processed data | Download |
+| --- | --- | --- |
+| [GSE135183](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE135183) | 18,582 genes × 30 RNA samples, 15 cases with two stromal compartments | [Raw counts, 606 KB compressed](https://ftp.ncbi.nlm.nih.gov/geo/series/GSE135nnn/GSE135183/suppl/GSE135183_raw_counts.csv.gz) |
+| [PXD023023](https://www.ebi.ac.uk/pride/archive/projects/PXD023023) | 1,583 native protein-group rows with 28 LFQ sample columns | [Protein groups, 2.8 MB](https://ftp.pride.ebi.ac.uk/pride/data/archive/2021/03/PXD023023/proteinGroups.txt) |
+| PXD023023 | 5,413 peptide rows with native quantitative fields | [Peptides, 4.5 MB](https://ftp.pride.ebi.ac.uk/pride/data/archive/2021/03/PXD023023/peptides.txt) |
+
+The downloaded protein and peptide files match PRIDE's deposited SHA-1 checksums;
+the audit also records SHA-256 for all three processed files. RNA values are
+nonnegative integer counts. Native protein-group counts include controls and
+contaminants and are not counts of confidently detected biological proteins.
+
+PRIDE filenames use case numbers 1–15; GEO uses case IDs such as 109 and 135.
+Matching the article's Table 1 to GEO by breed, age and histological subtype
+uniquely reconciles all 14 proteomics cases. The resulting 28 sample links are
+**metadata-derived**, not an author-supplied identifier crosswalk. Breed spelling
+normalizations are recorded. GEO case 127 is the unmatched RNA case.
+
+An importer must retain that pairing basis, separate stromal compartments,
+protein-group ambiguity, controls, missing quantities and native units. The
+deposited search used a dated canonical UniProt reference, but its FASTA is not
+among the 31 PRIDE files. Sequence/reference qualification remains necessary;
+these data do not establish ncORF translation. Author-derived contrasts in the
+supplementary workbooks must stay distinct from sample-level measurements.
+Import work remains tracked in [#20](https://github.com/openvax/orfdata/issues/20).
+
+## Dog Ribo-seq and ncORF translation
+
+The date-stamped dog-specific SRA, GEO and ENA queries in the audit returned no
+matching sequencing records. This is a bounded repository search, not proof
+that no unpublished or differently indexed experiment exists.
+
+[Pfeffer et al., 2015](https://www.nature.com/articles/ncomms9403)
+reports ribosome profiling and total RNA sequencing of canine pancreas rough-ER
+preparations aligned to CanFam3.1/Ensembl 77. Its accession section lists EMDB
+and PDB deposits, without a sequencing accession. No downloadable reads or
+processed ORF-level counts were verified in this audit. Even if recovered, the
+preparation would describe an enriched pancreatic compartment, not a broad
+normal-tissue canine translatome.
+
+Existing canine PeptideAtlas, Pfizer and DLA datasets retain their deposited
+canonical-search scope. The experimental dog ncORF search pipeline is a route
+to new analysis, not a released experimentally supported catalogue. Dog ncORF
+translation coverage therefore remains unavailable pending qualified data or
+a separately validated reanalysis. See [#12](https://github.com/openvax/orfdata/issues/12).

{orfdata-0.40.0 → orfdata-0.42.0}/docs/dog-peptides.md

@@ -5,6 +5,9 @@ spectrometry has observed. Neither searched for noncanonical ORFs, so they
 don't add ORFs to the dog proteome
 ([why dog has no ncORF catalogue](catalogs.md#dog)).
 
+For a verified paired RNA/protein study and the latest bounded search for dog
+Ribo-seq, see the [canine source audit](dog-data-sources.md).
+
 | Dataset | What it holds | How to get it |
 |---|---|---|
 | `kaabinejadian-dog-dla-ligands` | DLA class I ligands from four dog tumours and three DLA-88 monoallelic cell lines | `orfdata datasets download` (CC0, 25 MB) |

{orfdata-0.40.0 → orfdata-0.42.0}/docs/downloads.md

@@ -3,8 +3,48 @@
 ORFdata has one common entry point for data acquisition:
 
 ```sh
-orfdata download list
-orfdata download status
+orfdata data list
+orfdata data list --species dog
+orfdata data info pfizer-atlas-dog-peptide-evidence
+orfdata data fetch pfizer-atlas-dog-peptide-evidence
+orfdata data fetch peptideatlas-dog-peptides openprot-mouse
+orfdata data path pfizer-atlas-dog-peptide-evidence
+orfdata data status
+```
+
+`data`, `downloads` and `download` are aliases for the same command group.
+The `list/info/fetch/path` vocabulary follows other OpenVax download tools.
+`fetch` accepts one or more explicit resource names and chooses the registered
+acquisition route: download an artifact when available, otherwise build locally
+from checksum-pinned source files. All names and required terms are checked
+before the first acquisition. There is no implicit download-all operation.
+
+`info NAME` reports the version, source/coverage manifest and distribution
+metadata, including sizes and redistribution terms where declared. `path NAME`
+prints an installed file or directory for scripts; missing data is an error,
+and never triggers a download. Use `--verify` on reads to validate local bytes,
+`--cache-root DIR` to select a cache, and `--json` for machine output.
+`fetch --json` returns one result per distinct requested name.
+
+Use `--kind` to disambiguate colliding resource names. For one resource,
+`--version VERSION` selects a historical release and `--source-path ASSET=PATH`
+provides already downloaded catalogue/dataset sources or genome files. Source
+overrides remain checksum-checked. `--force` installs a fresh generation.
+Restricted chain downloads require `--accept-terms` after reviewing `info`.
+
+The same operations are available in Python:
+
+```python
+from orfdata import data_info, data_path, fetch_data
+
+details = data_info("openprot-mouse")  # Offline; shows the build route and terms.
+result = fetch_data("openprot-mouse")  # Explicit source download and processing.
+path = data_path("openprot-mouse")    # Offline file/directory lookup.
+```
+
+The focused forms remain available for additional resource-specific options:
+
+```sh
 orfdata download viral --species human
 orfdata download catalog NAME
 orfdata download dataset NAME
@@ -14,8 +54,7 @@ orfdata download chains --species human
 ```
 
 The operation comes first so the same discovery and installation model applies
-to every resource kind. `orfdata download viral` is therefore the primary
-command. Focused command groups such as `orfdata viral coverage` and
+to every resource kind. Focused command groups such as `orfdata viral coverage` and
 `orfdata viral summary` remain useful for domain-specific inspection.
 
 `list` shows every bundled, downloadable or locally buildable primary resource

{orfdata-0.40.0 → orfdata-0.42.0}/docs/human-tissue.md

@@ -17,7 +17,7 @@ yeast data.
 The download is approximately 397 MB and installs to a 3.86 GB SQLite database.
 
 ```sh
-pip install 'orfdata[data]'
+pip install 'orfdata'
 orfdata datasets download wang-human-tissue-abundance --version 2026-10-12.1
 ```
 

{orfdata-0.40.0 → orfdata-0.42.0}/docs/index.md

@@ -12,7 +12,7 @@ is a recorded host of the virus.
 Use Python 3.11 or later. Install orfdata and one PyEnsembl annotation:
 
 ```sh
-python -m pip install 'orfdata[pyensembl,build-data]'
+python -m pip install 'orfdata'
 pyensembl install --release 115 --species human
 orfdata setup --species human --catalogs all  # For ncORF presets and "all"
 ```

{orfdata-0.40.0 → orfdata-0.42.0}/docs/ingolia-yeast.md

@@ -6,7 +6,7 @@ measurements from [Ingolia et al. (2009)](https://doi.org/10.1126/science.116897
 It uses the same dataset API as human, mouse and dog.
 
 ```sh
-pip install 'orfdata[data]'
+pip install 'orfdata'
 orfdata datasets info ingolia-yeast-rna-ribo
 orfdata datasets download ingolia-yeast-rna-ribo
 ```
@@ -56,7 +56,7 @@ libraries and creates no assay pairs or translation-efficiency ratios. It also
 does not pair these cultures with the separate [CoPY protein study](copy-yeast.md).
 [Issue #11](https://github.com/openvax/orfdata/issues/11) tracks these source gaps.
 
-To rebuild, install `orfdata[data,build-data]` and run
+To rebuild, install `orfdata` and run
 `orfdata datasets build ingolia-yeast-rna-ribo`, or
 `DatasetRegistry().build("ingolia-yeast-rna-ribo")`. All 17 source inputs have
 pinned URLs, sizes and checksums. Verified local inputs can be supplied through

{orfdata-0.40.0 → orfdata-0.42.0}/docs/measurements.md

@@ -23,7 +23,7 @@ Its pooled PSM counts describe spectra, not sample-level protein abundance.
 
 ## Discover, download and query
 
-Install `orfdata[data]` to manage datasets. Creating a registry and listing
+Install `orfdata` to manage datasets. Creating a registry and listing
 releases reads metadata only:
 
 ```python
@@ -252,7 +252,7 @@ composite foreign keys, so human, mouse, dog, yeast and arbitrary other taxa use
 the same schema. [Compact storage and compatibility](storage.md) describes new
 SQLite v4 writes, legacy readers and actual-source size/query benchmarks.
 
-The core API needs neither pandas nor PyArrow. The optional `orfdata[columnar]`
-extra enables `dataset.export_parquet(path)`. Its query columns accompany the
+The normal installation includes pandas and PyArrow. Use
+`dataset.export_parquet(path)` to export query columns alongside the
 full measurement JSON, preserving exact values and provenance even when a
 floating-point analysis column cannot represent an integer exactly.

{orfdata-0.40.0 → orfdata-0.42.0}/docs/pfizer-protein.md

@@ -21,7 +21,7 @@ copies per cell. These are pooled tissue samples; rodent condition labels also
 include sex. Channels and technical runs do not count as independent donors.
 
 ```sh
-pip install 'orfdata[data]'
+pip install 'orfdata'
 orfdata datasets list --species dog
 orfdata datasets download pfizer-atlas-dog-protein
 orfdata datasets query pfizer-atlas-dog-protein --quantity protein_abundance --unit iBAQ --scale linear

{orfdata-0.40.0 → orfdata-0.42.0}/docs/pfizer-rna.md

@@ -19,7 +19,7 @@ Zeros stay measured zeros: 4,218,202 dog observations and 18,019,555 mouse
 observations. Every value retains the native numeric text and source line.
 
 ```sh
-pip install 'orfdata[data]'
+pip install 'orfdata'
 orfdata datasets download pfizer-atlas-dog-rna --version 2026-10-12.1
 orfdata datasets query pfizer-atlas-dog-rna --sample 1 --unit counts
 ```
@@ -74,7 +74,7 @@ and remain candidates for separate releases through the same importer.
 
 `registry.build(name, source_paths=...)` or `orfdata datasets build NAME` rebuilds
 from pinned counts, GEO metadata, factual Table S5 sample records and the
-historical GTF; workbook rebuilding needs `orfdata[build-data]`. Python returns
+historical GTF. Python returns
 a `QuantitativeDataset` ready to query. Reopen it offline with
 `registry.open_build(name)` or inspect it with `registry.inspect_build(name)`.
 The CLI selects that source build explicitly with `orfdata datasets query NAME

{orfdata-0.40.0 → orfdata-0.42.0}/mkdocs.yml

@@ -44,6 +44,7 @@ nav:
       - Yeast protein and RNA: copy-yeast.md
       - Yeast RNA and ribosome occupancy: ingolia-yeast.md
       - Dog MHC ligands and PeptideAtlas: dog-peptides.md
+      - Dog paired-data and Ribo-seq source audit: dog-data-sources.md
   - Project:
       - Release notes: https://github.com/openvax/orfdata/blob/main/CHANGELOG.md
       - Data roadmap: https://github.com/openvax/orfdata/issues/3

{orfdata-0.40.0 → orfdata-0.42.0}/orfdata/__init__.py

@@ -17,6 +17,7 @@ from .catalog import (
 )
 from .catalog_manifest import CatalogManifest
 from .catalogs import CatalogRegistry, build_catalog
+from .data_resources import data_info, data_path, fetch_data
 from .dataset import QuantitativeDataset
 from .datasets import DatasetRegistry, build_dataset
 from .downloads import DataStatus, list_data
@@ -176,6 +177,9 @@ __all__ = [
     "build_dataset",
     "DataStatus",
     "list_data",
+    "data_info",
+    "data_path",
+    "fetch_data",
     "DatasetManifest",
     "SourceAsset",
     "Sample",

{orfdata-0.40.0 → orfdata-0.42.0}/orfdata/catalog.py

@@ -1040,10 +1040,7 @@ def load_catalog(path=None, *, species=None, genome_build=None, registry=None, e
     root = getattr(registry, "_cache_root", None)
     needs = [_install_hint(c) for c, _ in plan if c.registry is not None and _installed(c) in (None, "damaged")]
     chains = list(dict.fromkeys(c for _, route in plan for c in route))
-    try:
-        missing = [c for c in chains if not chain_downloaded(c, cache_root=root)]
-    except ImportError:  # Without DataCache no chain can have been downloaded.
-        missing = chains
+    missing = [c for c in chains if not chain_downloaded(c, cache_root=root)]
     cli_root = "" if root is None else f" --cache-root {root}"
     if missing:
         accept = " --accept-terms" if any(c.restricted for c in missing) else ""
@@ -1052,17 +1049,10 @@ def load_catalog(path=None, *, species=None, genome_build=None, registry=None, e
                      f"download_chains(species={species!r}{', accept_terms=True' if accept else ''}"
                      f"{'' if root is None else f', cache_root={str(root)!r}'})")
     if needs:
-        try:
-            from .datasets import _datacache
-
-            _datacache()
-            step = ""
-        except ImportError:
-            step = "orfdata[data] installed, then "
         accept = " --accept-terms" if any(c.restricted for c in missing) else ""
         chosen = ("" if catalogs is None else " --catalogs " + (
             catalogs if isinstance(catalogs, str) else ",".join(catalogs)))
-        raise ValueError(f"{species} {genome_build} ORFs need {step}" + "; and ".join(needs)
+        raise ValueError(f"{species} {genome_build} ORFs need " + "; and ".join(needs)
                          + f". Or install everything at once with 'orfdata setup --species {species}{chosen}{accept}"
                          f"{cli_root}'")
     # Lifting and merging take seconds; one process reuses the result for exactly the same inputs.
@@ -1235,16 +1225,13 @@ def _releases(found):
 def _installed(choice):
     """How a registered release is installed: "downloaded", "built", "damaged" or None. Offline, unhashed."""
     registry, name, version = choice.registry, choice.name, choice.version
-    try:
-        damaged = False
-        if registry.published(name, version):
-            status = registry.inspect(name, version, verify_files=False).status
-            if status == "available":
-                return "downloaded"
-            damaged = status != "missing"
-        status = registry.inspect_build(name, version, verify_files=False).status
-    except ImportError:  # Without DataCache nothing can have been downloaded or built.
-        return None
+    damaged = False
+    if registry.published(name, version):
+        status = registry.inspect(name, version, verify_files=False).status
+        if status == "available":
+            return "downloaded"
+        damaged = status != "missing"
+    status = registry.inspect_build(name, version, verify_files=False).status
     if status == "available":
         return "built"
     return "damaged" if damaged or status != "missing" else None
@@ -1260,12 +1247,6 @@ def _open_registered(choice, expected_sha256):
         how = (f"{verb} it{when} with CatalogRegistry().{verb}({name!r}, {version!r}"
                f"{', force=True' if installed else ''}) or 'orfdata catalogs {verb} {name} --version {version}"
                f"{' --force' if installed else ''}'")
-        try:
-            from .datasets import _datacache
-
-            _datacache()
-        except ImportError:
-            how = "install orfdata[data], then " + how
         state = "damaged" if installed else "not installed"
         raise ValueError(f"The {name} {version} ORF catalogue is {state}; {how}")
     if installed == "built":
@@ -1334,10 +1315,7 @@ def catalog_status(*, registry=None):
         return plans[species, build, catalogs]
 
     def downloaded(chain):
-        try:
-            return chain_downloaded(chain, cache_root=root)
-        except ImportError:  # Without DataCache nothing can be downloaded.
-            return False
+        return chain_downloaded(chain, cache_root=root)
 
     rows = []
     for c in choices:

{orfdata-0.40.0 → orfdata-0.42.0}/orfdata/cli.py

@@ -30,10 +30,10 @@ def run(argv=None, prog=None, *, catalog_loader=load_catalog):
         from .proteome_cli import run as proteome_run
 
         return proteome_run(argv[1:], prog=(prog or "orfdata") + " proteome")
-    if argv and argv[0] == "download":
+    if argv and argv[0] in ("data", "download", "downloads"):
         from .download_cli import run as download_run
 
-        return download_run(argv[1:], prog=(prog or "orfdata") + " download")
+        return download_run(argv[1:], prog=f"{prog or 'orfdata'} {argv[0]}")
     if argv and argv[0] == "viral":
         from .viral_cli import run as viral_run
 
@@ -56,7 +56,7 @@ def run(argv=None, prog=None, *, catalog_loader=load_catalog):
                "catalogues with 'orfdata catalogs --help'; lift a catalogue to another assembly with "
                "'orfdata lift --help' and 'orfdata chains --help'; annotations PyEnsembl lacks, such as "
                "T2T-CHM13, with 'orfdata genomes --help'; discover and acquire data with "
-               "'orfdata download --help'; viral coverage, subsets and installed layers with "
+               "'orfdata data --help' (also 'downloads' or 'download'); viral coverage, subsets and installed layers with "
                "'orfdata viral --help'.")
     _add_query_arguments(parser)
     args = parser.parse_args(argv)

{orfdata-0.40.0 → orfdata-0.42.0}/orfdata/data/viral/NOTICE.md

@@ -137,7 +137,7 @@ GDC DNA is the source circle rotated by 864 bases. Both placements retain
 their own SHA256 and ordered, 1-based inclusive coding blocks.
 GDC reference files: https://gdc.cancer.gov/about-data/gdc-data-processing/gdc-reference-files .
 
-Rebuild with `orfdata[build-data]` installed:
+Rebuild with `orfdata` installed:
 
 ```sh
 python tools/build_hpv16_cds.py tests/data/viral/NC_001526.4.gb.gz \