vcf-subset 2.0.0__tar.gz → 2.0.2__tar.gz

vcf_subset-2.0.2/.github/workflows/gitleaks.yml

@@ -0,0 +1,20 @@
+on:
+  pull_request:
+    branches:
+      - develop
+      - main
+  push:
+    tags:
+      - '*.*.*'
+      - '*.*.*-rc*'
+
+jobs:
+  gitleaks:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+        with:
+            fetch-depth: 0
+
+      - name: Check for GitLeaks
+        uses: gacts/gitleaks@v1

vcf_subset-2.0.0/.github/workflows/CI.yml → vcf_subset-2.0.2/.github/workflows/release.yml

@@ -1,9 +1,9 @@
-# This file is autogenerated by maturin v1.7.4
+# This file is autogenerated by maturin v1.7.0
 # To update, run
 #
 #    maturin generate-ci github
 #
-name: CI
+name: Release package
 
 on:
   release:
@@ -13,6 +13,17 @@ permissions:
   contents: read
 
 jobs:
+  cargo:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - uses: actions-rs/toolchain@v1
+        with:
+            toolchain: stable
+            override: true
+      - uses: katyo/publish-crates@v2
+        with:
+            registry-token: ${{ secrets.CARGO_REGISTRY_TOKEN }}
   linux:
     runs-on: ${{ matrix.platform.runner }}
     strategy:
@@ -20,7 +31,9 @@ jobs:
         platform:
           - runner: ubuntu-latest
             target: x86_64
-          - runner: ubuntu-latest
+          # The manylinux2014 i686 container can't resolve vault.centos.org on
+          # ubuntu-26.04. See https://github.com/PyO3/maturin-action/issues/484
+          - runner: ubuntu-24.04
             target: x86
           - runner: ubuntu-latest
             target: aarch64
@@ -79,59 +92,6 @@ jobs:
           name: wheels-musllinux-${{ matrix.platform.target }}
           path: dist
 
-  windows:
-    runs-on: ${{ matrix.platform.runner }}
-    strategy:
-      matrix:
-        platform:
-          - runner: windows-latest
-            target: x64
-          - runner: windows-latest
-            target: x86
-    steps:
-      - uses: actions/checkout@v4
-      - uses: actions/setup-python@v5
-        with:
-          python-version: 3.x
-          architecture: ${{ matrix.platform.target }}
-      - name: Build wheels
-        uses: PyO3/maturin-action@v1
-        with:
-          target: ${{ matrix.platform.target }}
-          args: --release --out dist --find-interpreter
-          sccache: 'true'
-      - name: Upload wheels
-        uses: actions/upload-artifact@v4
-        with:
-          name: wheels-windows-${{ matrix.platform.target }}
-          path: dist
-
-  macos:
-    runs-on: ${{ matrix.platform.runner }}
-    strategy:
-      matrix:
-        platform:
-          - runner: macos-12
-            target: x86_64
-          - runner: macos-14
-            target: aarch64
-    steps:
-      - uses: actions/checkout@v4
-      - uses: actions/setup-python@v5
-        with:
-          python-version: 3.x
-      - name: Build wheels
-        uses: PyO3/maturin-action@v1
-        with:
-          target: ${{ matrix.platform.target }}
-          args: --release --out dist --find-interpreter
-          sccache: 'true'
-      - name: Upload wheels
-        uses: actions/upload-artifact@v4
-        with:
-          name: wheels-macos-${{ matrix.platform.target }}
-          path: dist
-
   sdist:
     runs-on: ubuntu-latest
     steps:
@@ -150,23 +110,11 @@ jobs:
   release:
     name: Release
     runs-on: ubuntu-latest
-    if: ${{ startsWith(github.ref, 'refs/tags/') || github.event_name == 'workflow_dispatch' }}
-    needs: [linux, musllinux, windows, macos, sdist]
-    permissions:
-      # Use to sign the release artifacts
-      id-token: write
-      # Used to upload release artifacts
-      contents: write
-      # Used to generate artifact attestation
-      attestations: write
+    if: "startsWith(github.ref, 'refs/tags/')"
+    needs: [linux, musllinux, sdist]
     steps:
       - uses: actions/download-artifact@v4
-      - name: Generate artifact attestation
-        uses: actions/attest-build-provenance@v1
-        with:
-          subject-path: 'wheels-*/*'
       - name: Publish to PyPI
-        if: "startsWith(github.ref, 'refs/tags/')"
         uses: PyO3/maturin-action@v1
         env:
           MATURIN_PYPI_TOKEN: ${{ secrets.PYPI_API_TOKEN }}

{vcf_subset-2.0.0 → vcf_subset-2.0.2}/Cargo.lock

@@ -1,18 +1,6 @@
 # This file is automatically @generated by Cargo.
 # It is not intended for manual editing.
-version = 3
-
-[[package]]
-name = "autocfg"
-version = "1.4.0"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "ace50bade8e6234aa140d9a2f552bbee1db4d353f69b8217bc503490fc1a9f26"
-
-[[package]]
-name = "cfg-if"
-version = "1.0.0"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "baf1de4339761588bc0619e3cbc0120ee582ebb74b53b4efbf79117bd2da40fd"
+version = 4
 
 [[package]]
 name = "heck"
@@ -20,35 +8,17 @@ version = "0.5.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "2304e00983f87ffb38b55b444b5e3b60a884b5d30c0fca7d82fe33449bbe55ea"
 
-[[package]]
-name = "indoc"
-version = "2.0.5"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "b248f5224d1d606005e02c97f5aa4e88eeb230488bcc03bc9ca4d7991399f2b5"
-
 [[package]]
 name = "libc"
 version = "0.2.159"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "561d97a539a36e26a9a5fad1ea11a3039a67714694aaa379433e580854bc3dc5"
 
-[[package]]
-name = "memoffset"
-version = "0.9.1"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "488016bfae457b036d996092f6cb448677611ce4449e970ceaf42695203f218a"
-dependencies = [
- "autocfg",
-]
-
 [[package]]
 name = "once_cell"
-version = "1.20.1"
+version = "1.21.4"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "82881c4be219ab5faaf2ad5e5e5ecdff8c66bd7402ca3160975c93b24961afd1"
-dependencies = [
- "portable-atomic",
-]
+checksum = "9f7c3e4beb33f85d45ae3e3a1792185706c8e16d043238c593331cc7cd313b50"
 
 [[package]]
 name = "portable-atomic"
@@ -58,46 +28,41 @@ checksum = "cc9c68a3f6da06753e9335d63e27f6b9754dd1920d941135b7ea8224f141adb2"
 
 [[package]]
 name = "proc-macro2"
-version = "1.0.86"
+version = "1.0.107"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "5e719e8df665df0d1c8fbfd238015744736151d4445ec0836b8e628aae103b77"
+checksum = "985e7ec9bb745e6ce6535b544d84d6cd6f7ad8bd711c398938ae983b91a766d9"
 dependencies = [
  "unicode-ident",
 ]
 
 [[package]]
 name = "pyo3"
-version = "0.22.3"
+version = "0.30.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "15ee168e30649f7f234c3d49ef5a7a6cbf5134289bc46c29ff3155fa3221c225"
+checksum = "229ca13b8a15bb0d1487b81ab975bfcd97513416499a8312011b6036e42e0de4"
 dependencies = [
- "cfg-if",
- "indoc",
  "libc",
- "memoffset",
  "once_cell",
  "portable-atomic",
  "pyo3-build-config",
  "pyo3-ffi",
  "pyo3-macros",
- "unindent",
 ]
 
 [[package]]
 name = "pyo3-build-config"
-version = "0.22.3"
+version = "0.30.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "e61cef80755fe9e46bb8a0b8f20752ca7676dcc07a5277d8b7768c6172e529b3"
+checksum = "70130e2b6dd1ee589a8788026a429561ca5c40fa7a2fa7914c2282eddae24700"
 dependencies = [
- "once_cell",
  "target-lexicon",
 ]
 
 [[package]]
 name = "pyo3-ffi"
-version = "0.22.3"
+version = "0.30.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "67ce096073ec5405f5ee2b8b31f03a68e02aa10d5d4f565eca04acc41931fa1c"
+checksum = "5e7ff73c555c286d212d4ce7e5fbda845a973c4f61bd5f160f5f2c3c2a04d1c4"
 dependencies = [
  "libc",
  "pyo3-build-config",
@@ -105,9 +70,9 @@ dependencies = [
 
 [[package]]
 name = "pyo3-macros"
-version = "0.22.3"
+version = "0.30.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "2440c6d12bc8f3ae39f1e775266fa5122fd0c8891ce7520fa6048e683ad3de28"
+checksum = "c46d2e5862c7bb8207e3b639f713dda3c499933444784154c11d013c5a691b60"
 dependencies = [
  "proc-macro2",
  "pyo3-macros-backend",
@@ -117,13 +82,12 @@ dependencies = [
 
 [[package]]
 name = "pyo3-macros-backend"
-version = "0.22.3"
+version = "0.30.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "1be962f0e06da8f8465729ea2cb71a416d2257dff56cbe40a70d3e62a93ae5d1"
+checksum = "38b89f066f2ae72a2aef52d1537ca2fcd104440ebfadee06e97aa90738a25b9b"
 dependencies = [
  "heck",
  "proc-macro2",
- "pyo3-build-config",
  "quote",
  "syn",
 ]
@@ -139,9 +103,9 @@ dependencies = [
 
 [[package]]
 name = "syn"
-version = "2.0.79"
+version = "3.0.10"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "89132cd0bf050864e1d38dc3bbc07a0eb8e7530af26344d3d2bbbef83499f590"
+checksum = "4ae9ccbea3a7b0b09443036490c8f34a8b1b760fd345e5c0dae0aac718faea79"
 dependencies = [
  "proc-macro2",
  "quote",
@@ -150,9 +114,9 @@ dependencies = [
 
 [[package]]
 name = "target-lexicon"
-version = "0.12.16"
+version = "0.13.5"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "61c41af27dd6d1e27b1b16b489db798443478cef1f06a660c96db617ba5de3b1"
+checksum = "adb6935a6f5c20170eeceb1a3835a49e12e19d792f6dd344ccc76a985ca5a6ca"
 
 [[package]]
 name = "unicode-ident"
@@ -160,15 +124,9 @@ version = "1.0.13"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "e91b56cd4cadaeb79bbf1a5645f6b4f8dc5bde8834ad5894a8db35fda9efa1fe"
 
-[[package]]
-name = "unindent"
-version = "0.2.3"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "c7de7d73e1754487cb58364ee906a499937a0dfabd86bcb980fa99ec8c8fa2ce"
-
 [[package]]
 name = "vcf_subset"
-version = "2.0.0"
+version = "2.0.2"
 dependencies = [
  "pyo3",
 ]

{vcf_subset-2.0.0 → vcf_subset-2.0.2}/Cargo.toml

@@ -1,7 +1,8 @@
 [package]
 name = "vcf_subset"
-version = "2.0.0"
+version = "2.0.2"
 edition = "2021"
+readme = "README.md"
 
 # See more keys and their definitions at https://doc.rust-lang.org/cargo/reference/manifest.html
 [lib]
@@ -9,7 +10,7 @@ name = "vcf_subset"
 crate-type = ["cdylib"]
 
 [dependencies]
-pyo3 = "0.22.0"
+pyo3 = { version = "0.30", features = ["extension-module", "abi3-py39", "abi3-py310", "abi3-py311", "abi3-py312", "abi3-py313"] }
 
 [profile.dev]
 opt-level = 3

vcf_subset-2.0.2/LICENSE

@@ -0,0 +1,85 @@
+LICENCE TERMS FOR ACCESS TO SOFTWARE AND DATABASE FOR ACADEMIC USE
+
+These licence terms apply to all licences granted by THE CHANCELLOR, MASTERS AND SCHOLARS OF THE UNIVERSITY
+OF OXFORD whose administrative offices are at University Offices, Wellington Square, Oxford OX1 2JD,
+United Kingdom (the "University") for use of or access to vcf_subset software ("the Software")
+through this website (the "Website").
+
+PLEASE READ THESE LICENCE TERMS CAREFULLY BEFORE USING THE DATABASE OR THE SOFTWARE THROUGH THIS WEBSITE.
+IF YOU DO NOT AGREE TO THESE LICENCE TERMS YOU SHOULD NOT DOWNLOAD OR USE THE SOFTWARE.
+
+THE SOFTWARE ARE INTENDED FOR ACADEMICS CARRYING OUT RESEARCH AND NOT FOR USE BY CONSUMERS OR COMMERCIAL BUSINESSES.
+
+1.	Academic Use Licence
+
+1.1	The User is granted a limited non-exclusive and non-transferable royalty free licence to access and
+use the Software provided that the User will:
+
+(a)	limit their use of the Software to their own internal academic non-commercial research which is
+undertaken for the purposes of education or other scholarly use;
+
+(b)	not use the Software for or on behalf of any third party or to provide a service or integrate all
+or part of the Software into a product for sale or license to third parties;
+
+(c)	use the Software in accordance with the prevailing instructions and guidance for use given on the
+Website and comply with procedures on the Website for user identification, authentication and access;
+
+(d)	comply with all applicable laws and regulations with respect to their use of the Software;
+
+(e)	except to the extent expressly permitted under these terms, not attempt to: reverse compile, disassemble
+or copy, modify, duplicate, create derivative works from, frame, mirror, republish, download, display, transmit,
+or distribute all or any portion of the Software or Website in any form or media or by any means; and
+
+(f)	ensure that the Copyright Notice “Copyright © 2022, University of Oxford” appears prominently wherever
+results from the Software are used, and is referenced or cited with the Copyright Notice when the Software
+is described in any research publication or on any documents or other material created using the Software.
+
+1.2	the University reserves the right at any time and without liability or prior notice to the User to
+revise, modify and replace the functionality and performance of the access to and operation of the Software.
+
+1.3	The User acknowledges and agrees that the University owns all intellectual property rights in the Software.
+The User shall not have any right, title or interest in or to any results or other output from the Software.
+
+1.4	This Licence will terminate immediately and the User will no longer have any right exercise any of the
+rights granted to the User upon any breach of the conditions in Section 1.1 of this Licence.
+
+2.	Indemnity and Liability
+
+2.1	The User shall defend, indemnify and hold harmless the University against any claims, actions, proceedings,
+losses, damages, expenses and costs (including without limitation court costs and reasonable legal fees) arising
+out of or in connection with the User's possession or use of the Software, or any breach of these terms by the User.
+
+2.2	The Software are provided on an ‘as is’ basis and the User uses the Software at their own risk. No representations,
+conditions, warranties or other terms of any kind are given in respect of the Software and all statutory warranties
+and conditions are excluded to the fullest extent permitted by law. Without affecting the generality of the previous
+sentences, the University gives no implied or express warranty and makes no representation that the Software or
+any part of them: (a) will enable specific results to be obtained; or (b) meets a particular specification or is
+comprehensive within its field or that it is error free or will operate without interruption; or (c) is suitable
+for any particular, or the User's specific purposes.
+
+2.3	Except in relation to fraud, death or personal injury, the University's liability to the User for any use of
+the Software, in negligence or arising in any other way out of the subject matter of these licence terms, will not
+extend to any incidental or consequential damages or losses, or any loss of profits, loss of revenue, loss of data,
+loss of contracts or opportunity, whether direct or indirect.
+
+2.4	The User hereby irrevocably undertakes to the University not to make any claim against any employee, student,
+researcher or other individual engaged by the University, being a claim which seeks to enforce against any of them
+any liability whatsoever in connection with this agreement or its subject-matter.
+
+3.	General
+
+3.1	Severability - If any provision (or part of a provision) of these licence terms is found by any court or
+administrative body of competent jurisdiction to be invalid, unenforceable or illegal, the other provisions shall
+remain in force.
+
+3.2	Entire Agreement - These licence terms and any documents referred to in them, constitute the whole agreement
+between the parties and supersede any previous arrangement, understanding or agreement between them relating to
+the Software.
+
+3.3	Law and Jurisdiction - These licence terms and any disputes or claims arising out of or in connection with them
+shall be governed by, and construed in accordance with, the law of England. The User irrevocably submits to the
+exclusive jurisdiction of the English courts for any dispute or claim that arises out of or in connection with
+these licence terms.
+
+If you are interested in using the Software commercially, please contact Oxford University Innovation Limited to
+negotiate a licence. Contact details are enquiries@innovation.ox.ac.uk quoting reference (TBD).

vcf_subset-2.0.2/PKG-INFO

@@ -0,0 +1,8 @@
+Metadata-Version: 2.4
+Name: vcf_subset
+Version: 2.0.2
+Classifier: Programming Language :: Rust
+Classifier: Programming Language :: Python :: Implementation :: CPython
+Classifier: Programming Language :: Python :: Implementation :: PyPy
+License-File: LICENSE
+Requires-Python: >=3.8, <3.13

{vcf_subset-2.0.0 → vcf_subset-2.0.2}/README.md

@@ -1,5 +1,7 @@
 # vcf_subset
-Efficient VCF subsetting by genome position. Written in Rust, but provided as a python module to save ~3 minutes per TB GVCF
+Efficient VCF subsetting by genome position. Written in Rust, but provided as a python module to save ~3 minutes per TB GVCF. This code
+is functionall part of `gnomonicus` but is in a seperate repository
+so it can effecitvely be a python package.
 
 ## Install
 ```

{vcf_subset-2.0.0 → vcf_subset-2.0.2}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "maturin"
 
 [project]
 name = "vcf_subset"
-requires-python = ">=3.8"
+requires-python = ">=3.8,<3.13"
 classifiers = [
     "Programming Language :: Rust",
     "Programming Language :: Python :: Implementation :: CPython",

vcf_subset-2.0.0/PKG-INFO

@@ -1,27 +0,0 @@
-Metadata-Version: 2.3
-Name: vcf_subset
-Version: 2.0.0
-Classifier: Programming Language :: Rust
-Classifier: Programming Language :: Python :: Implementation :: CPython
-Classifier: Programming Language :: Python :: Implementation :: PyPy
-Requires-Python: >=3.8
-Description-Content-Type: text/markdown; charset=UTF-8; variant=GFM
-
-# vcf_subset
-Efficient VCF subsetting by genome position. Written in Rust, but provided as a python module to save ~3 minutes per TB GVCF
-
-## Install
-```
-pip install vcf_subset
-```
-
-## Local (dev) install
-```
-# Optional virtual environment
-python -m virtualenv env
-source env/bin/activate
-
-# Install
-pip install .
-```
-