diff --git a/docs/project/changelog.md b/docs/project/changelog.md index 173646a62..d651b63c6 100644 --- a/docs/project/changelog.md +++ b/docs/project/changelog.md @@ -26,6 +26,11 @@ myst: a single file. {pr}`3727` +### Packages + +- New packages: sourmash {pr}`3635`, screed {pr}`3635`, bitstring {pr}`3635`, + deprecation {pr}`3635`, cachetools {pr}`3635`. + ## Version 0.23.0 _March 30, 2023_ diff --git a/packages/bitstring/meta.yaml b/packages/bitstring/meta.yaml new file mode 100644 index 000000000..0fd70091b --- /dev/null +++ b/packages/bitstring/meta.yaml @@ -0,0 +1,13 @@ +package: + name: bitstring + version: 4.0.1 + top-level: + - bitstring +source: + url: https://files.pythonhosted.org/packages/1b/07/951d7bc9804fcec26e8cdbf1d352018a21c16194d42e3f38cb7f5564ca4b/bitstring-4.0.1-py3-none-any.whl + sha256: 4a27cdefd95eb535c4b79e0afcdb5532ba1dba0aaed98a31ad98f46b1e0d5bd9 +about: + home: "" + PyPI: https://pypi.org/project/bitstring + summary: Simple construction, analysis and modification of binary data. + license: "" diff --git a/packages/cachetools/meta.yaml b/packages/cachetools/meta.yaml new file mode 100644 index 000000000..988b85e59 --- /dev/null +++ b/packages/cachetools/meta.yaml @@ -0,0 +1,13 @@ +package: + name: cachetools + version: 5.3.0 + top-level: + - cachetools +source: + url: https://files.pythonhosted.org/packages/db/14/2b48a834d349eee94677e8702ea2ef98b7c674b090153ea8d3f6a788584e/cachetools-5.3.0-py3-none-any.whl + sha256: 429e1a1e845c008ea6c85aa35d4b98b65d6a9763eeef3e37e92728a12d1de9d4 +about: + home: https://github.com/tkem/cachetools/ + PyPI: https://pypi.org/project/cachetools + summary: Extensible memoizing collections and decorators + license: MIT diff --git a/packages/deprecation/meta.yaml b/packages/deprecation/meta.yaml new file mode 100644 index 000000000..e5e7b63cd --- /dev/null +++ b/packages/deprecation/meta.yaml @@ -0,0 +1,16 @@ +package: + name: deprecation + version: 2.1.0 + top-level: + - deprecation +requirements: + run: + - packaging +source: + url: https://files.pythonhosted.org/packages/02/c3/253a89ee03fc9b9682f1541728eb66db7db22148cd94f89ab22528cd1e1b/deprecation-2.1.0-py2.py3-none-any.whl + sha256: a10811591210e1fb0e768a8c25517cabeabcba6f0bf96564f8ff45189f90b14a +about: + home: http://deprecation.readthedocs.io/ + PyPI: https://pypi.org/project/deprecation + summary: A library to handle automated deprecations + license: Apache 2 diff --git a/packages/screed/meta.yaml b/packages/screed/meta.yaml new file mode 100644 index 000000000..de29570a5 --- /dev/null +++ b/packages/screed/meta.yaml @@ -0,0 +1,14 @@ +package: + name: screed + version: 1.1.2 + top-level: + - bigtests + - screed +source: + url: https://files.pythonhosted.org/packages/a6/c1/e33d75369bffaf304b891afa34aa8b9765f117931673cdf8837eba9b0efb/screed-1.1.2-py2.py3-none-any.whl + sha256: 413e9cfce4b4908d0fa1fe69dcd2c523641a02a856eb196f9ce2183657f342dc +about: + home: https://github.com/dib-lab/screed + PyPI: https://pypi.org/project/screed + summary: a Python library for loading FASTA and FASTQ sequences + license: BSD 3-clause diff --git a/packages/sourmash/meta.yaml b/packages/sourmash/meta.yaml new file mode 100644 index 000000000..191904d08 --- /dev/null +++ b/packages/sourmash/meta.yaml @@ -0,0 +1,28 @@ +package: + name: sourmash + version: 4.8.0 + top-level: + - sourmash +requirements: + run: + - screed + - cffi + - deprecation + - cachetools + - numpy + - matplotlib + - scipy + - sqlite3 + - bitstring +source: + url: https://pypi.io/packages/source/s/sourmash/sourmash-4.8.0.tar.gz + sha256: 778d5d182f9e625ae560a5b3a2fdf6bd4fd3b876c84593da8c8c07d11ce2c697 +build: + script: | + rustup toolchain install ${RUST_TOOLCHAIN} && rustup default ${RUST_TOOLCHAIN} + rustup target add wasm32-unknown-emscripten --toolchain ${RUST_TOOLCHAIN} +about: + home: https://github.com/sourmash-bio/sourmash + PyPI: https://pypi.org/project/sourmash + summary: Compute and compare MinHash signatures for DNA data sets. + license: BSD-3-Clause diff --git a/packages/sourmash/test_sourmash.py b/packages/sourmash/test_sourmash.py new file mode 100644 index 000000000..24b7226e9 --- /dev/null +++ b/packages/sourmash/test_sourmash.py @@ -0,0 +1,23 @@ +import pytest +from pytest_pyodide import run_in_pyodide + + +@pytest.mark.driver_timeout(60) +@run_in_pyodide(packages=["sourmash"]) +def test_simple_save_load(selenium): + from pathlib import Path + from tempfile import TemporaryDirectory + + import sourmash + + mh = sourmash.MinHash(0, 5, scaled=1) + mh.add_sequence("ACGTAGGTATAGGATACCTCGCTAGTACGTGCA") + ss = sourmash.SourmashSignature(mh, name="foo") + + with TemporaryDirectory() as td: + name = Path(td) / "test.sig" + with open(name, "w") as fp: + sourmash.save_signatures([ss], fp=fp) + + loaded = sourmash.load_one_signature(str(name)) + assert loaded == ss