bed-reader 0.2.36__tar.gz → 0.2.37__tar.gz

{bed_reader-0.2.36 → bed_reader-0.2.37}/.github/workflows/ci.yml

@@ -26,7 +26,7 @@ jobs:
     runs-on: ${{ matrix.os }}
     steps:
       - name: Checkout
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
       - name: Set up Rust
         uses: actions-rs/toolchain@v1
         with:
@@ -46,11 +46,11 @@ jobs:
       - uses: actions/setup-python@v4
         with:
           python-version: |
-            3.7
             3.8
             3.9
             3.10
             3.11
+            3.12
       - name: Build wheels
         uses: PyO3/maturin-action@v1
         with:
@@ -139,12 +139,12 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: [3.7, 3.8, 3.9, "3.10", "3.11"]
+        python-version: [3.8, 3.9, "3.10", "3.11", "3.12"]
         os: [ubuntu-latest, macos-latest, windows-latest]
     runs-on: ${{ matrix.os }}
     steps:
     - name: Checkout
-      uses: actions/checkout@v2
+      uses: actions/checkout@v3
     - uses: actions/setup-python@v4
       with:
         python-version: ${{ matrix.python-version }}

{bed_reader-0.2.36 → bed_reader-0.2.37}/Cargo.lock

@@ -86,7 +86,7 @@ checksum = "904dfeac50f3cdaba28fc6f57fdcddb75f49ed61346676a78c4ffe55877802fd"
 
 [[package]]
 name = "bed-reader"
-version = "0.2.36"
+version = "0.2.37"
 dependencies = [
  "anyinput",
  "approx 0.5.1",
@@ -501,9 +501,9 @@ dependencies = [
 
 [[package]]
 name = "indoc"
-version = "1.0.7"
+version = "2.0.4"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "adab1eaa3408fb7f0c777a73e7465fd5656136fc93b670eb6df3c88c2c1344e3"
+checksum = "1e186cfbae8084e513daff4240b4797e342f988cecda4fb6c939150f96315fd8"
 
 [[package]]
 name = "js-sys"
@@ -571,9 +571,9 @@ dependencies = [
 
 [[package]]
 name = "memoffset"
-version = "0.8.0"
+version = "0.9.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "d61c719bcfbcf5d62b3a09efa6088de8c54bc0bfcd3ea7ae39fcc186108b8de1"
+checksum = "5a634b1c61a95585bd15607c6ab0c4e5b226e695ff2800ba0cdccddf208c406c"
 dependencies = [
  "autocfg",
 ]
@@ -717,9 +717,9 @@ dependencies = [
 
 [[package]]
 name = "numpy"
-version = "0.18.0"
+version = "0.20.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "96b0fee4571867d318651c24f4a570c3f18408cf95f16ccb576b3ce85496a46e"
+checksum = "bef41cbb417ea83b30525259e30ccef6af39b31c240bda578889494c5392d331"
 dependencies = [
  "libc",
  "ndarray",
@@ -853,9 +853,9 @@ dependencies = [
 
 [[package]]
 name = "proc-macro2"
-version = "1.0.55"
+version = "1.0.69"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "1d0dd4be24fcdcfeaa12a432d588dc59bbad6cad3510c67e74a2b6b2fc950564"
+checksum = "134c189feb4956b20f6f547d2cf727d4c0fe06722b20a0eec87ed445a97f92da"
 dependencies = [
  "unicode-ident",
 ]
@@ -875,14 +875,14 @@ dependencies = [
 
 [[package]]
 name = "pyo3"
-version = "0.18.3"
+version = "0.20.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "e3b1ac5b3731ba34fdaa9785f8d74d17448cd18f30cf19e0c7e7b1fdb5272109"
+checksum = "04e8453b658fe480c3e70c8ed4e3d3ec33eb74988bd186561b0cc66b85c3bc4b"
 dependencies = [
  "cfg-if",
  "indoc",
  "libc",
- "memoffset 0.8.0",
+ "memoffset 0.9.0",
  "parking_lot",
  "pyo3-build-config",
  "pyo3-ffi",
@@ -892,9 +892,9 @@ dependencies = [
 
 [[package]]
 name = "pyo3-build-config"
-version = "0.18.3"
+version = "0.20.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "9cb946f5ac61bb61a5014924910d936ebd2b23b705f7a4a3c40b05c720b079a3"
+checksum = "a96fe70b176a89cff78f2fa7b3c930081e163d5379b4dcdf993e3ae29ca662e5"
 dependencies = [
  "once_cell",
  "target-lexicon",
@@ -902,9 +902,9 @@ dependencies = [
 
 [[package]]
 name = "pyo3-ffi"
-version = "0.18.3"
+version = "0.20.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "fd4d7c5337821916ea2a1d21d1092e8443cf34879e53a0ac653fbb98f44ff65c"
+checksum = "214929900fd25e6604661ed9cf349727c8920d47deff196c4e28165a6ef2a96b"
 dependencies = [
  "libc",
  "pyo3-build-config",
@@ -912,25 +912,26 @@ dependencies = [
 
 [[package]]
 name = "pyo3-macros"
-version = "0.18.3"
+version = "0.20.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "a9d39c55dab3fc5a4b25bbd1ac10a2da452c4aca13bb450f22818a002e29648d"
+checksum = "dac53072f717aa1bfa4db832b39de8c875b7c7af4f4a6fe93cdbf9264cf8383b"
 dependencies = [
  "proc-macro2",
  "pyo3-macros-backend",
  "quote",
- "syn 1.0.102",
+ "syn 2.0.13",
 ]
 
 [[package]]
 name = "pyo3-macros-backend"
-version = "0.18.3"
+version = "0.20.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "97daff08a4c48320587b5224cc98d609e3c27b6d437315bd40b605c98eeb5918"
+checksum = "7774b5a8282bd4f25f803b1f0d945120be959a36c72e08e7cd031c792fdfd424"
 dependencies = [
+ "heck",
  "proc-macro2",
  "quote",
- "syn 1.0.102",
+ "syn 2.0.13",
 ]
 
 [[package]]
@@ -1286,9 +1287,9 @@ dependencies = [
 
 [[package]]
 name = "unindent"
-version = "0.1.10"
+version = "0.2.3"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "58ee9362deb4a96cef4d437d1ad49cffc9b9e92d202b6995674e928ce684f112"
+checksum = "c7de7d73e1754487cb58364ee906a499937a0dfabd86bcb980fa99ec8c8fa2ce"
 
 [[package]]
 name = "untrusted"

{bed_reader-0.2.36 → bed_reader-0.2.37}/Cargo.toml

@@ -1,19 +1,25 @@
 # See more keys and their definitions at https://doc.rust-lang.org/cargo/reference/manifest.html
 
 [package]
-version = "0.2.36"
+version = "0.2.37"
 name = "bed-reader"
 description = "Read and write the PLINK BED format, simply and efficiently."
 repository = "https://github.com/fastlmm/bed-reader"
 readme = "README-rust.md"
 documentation = "https://docs.rs/bed-reader/latest/bed_reader/"
 authors = ["FaST-LMM Team <fastlmm-dev@python.org>"]
-exclude = ["tests/*", "doc/*", "docs/*"]
 license = "Apache-2.0"
 keywords = ["bioinformatics", "plink", "genomics", "genotype", "snps"]
 categories = ["science"]
 edition = "2021"
 homepage = "https://fastlmm.github.io/"
+exclude = [
+    "**/tests/data/*",
+    "doc/*",
+    "docs/*",
+    "target/*",
+    "**/target/debug/*",
+]
 
 
 [lib]
@@ -31,12 +37,12 @@ thiserror = "1.0.40"
 num-traits = "0.2.15"
 ndarray-npy = { version = "0.8.1", default-features = false }
 rayon = "1.7.0"
-numpy = "0.18.0"
+numpy = "0.20.0"
 ndarray = { version = "0.15.6", features = ["approx", "rayon"] }
 approx = "0.5.1"
 statrs = "0.16.0"
 byteorder = { version = "1.4.3", default-features = false }
-pyo3 = { version = "0.18.3", features = ["extension-module"], optional = true }
+pyo3 = { version = "0.20.0", features = ["extension-module"], optional = true }
 dpc-pariter = "0.4.0"                                                           # //  pariter = "0.5.1"
 derive_builder = "0.12.0"
 temp_testdir = "0.2.3"
@@ -52,4 +58,4 @@ fetch-data = "0.1.6"
 ndarray-rand = "0.14.0"
 
 [build-dependencies]
-pyo3-build-config = "0.18.3"
+pyo3-build-config = "0.20.0"

{bed_reader-0.2.36 → bed_reader-0.2.37}/PKG-INFO

@@ -1,11 +1,11 @@
 Metadata-Version: 2.1
 Name: bed-reader
-Version: 0.2.36
-Classifier: Programming Language :: Python :: 3.7
+Version: 0.2.37
 Classifier: Programming Language :: Python :: 3.8
 Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
 Classifier: Programming Language :: Python :: 3
 Classifier: Programming Language :: Python
 Requires-Dist: numpy>=1.13.3
@@ -22,9 +22,9 @@ Author-email: FaST-LMM Team <fastlmm-dev@python.org>
 License: Apache-2.0
 Description-Content-Type: text/markdown; charset=UTF-8; variant=GFM
 Project-URL: Source Code, https://github.com/fastlmm/bed-reader
-Project-URL: Documentation, http://fastlmm.github.io/bed-reader
 Project-URL: Homepage, https://fastlmm.github.io
 Project-URL: Bug Tracker, https://github.com/fastlmm/bed-reader/issues
+Project-URL: Documentation, http://fastlmm.github.io/bed-reader
 
 [![PyPI version](https://badge.fury.io/py/bed-reader.svg)](https://badge.fury.io/py/bed-reader)
 [![PyPI version](https://badge.fury.io/py/bed-reader.svg)](https://badge.fury.io/py/bed-reader)

{bed_reader-0.2.36 → bed_reader-0.2.37}/bed_reader/_open_bed.py

@@ -39,7 +39,7 @@ def _sequence(key, length, missing, dtype):
         longest = len(f"{key}{length}")
         dtype = f"<U{longest}"
     return np.fromiter(
-        (f"{key}{i+1}" for i in range(length)), dtype=dtype, count=length
+        (f"{key}{i + 1}" for i in range(length)), dtype=dtype, count=length
     )
 
 

{bed_reader-0.2.36 → bed_reader-0.2.37}/pyproject.toml

@@ -2,15 +2,20 @@
 name = "bed-reader"
 readme = "README.md"
 classifiers = [
-    "Programming Language :: Python :: 3.7",
     "Programming Language :: Python :: 3.8",
     "Programming Language :: Python :: 3.9",
     "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
     "Programming Language :: Python :: 3",
     "Programming Language :: Python",
 ]
-dependencies = ["numpy>=1.13.3", "pandas>=0.25.1", "pooch>=1.4.0", "chardet>=5.1.0"]
+dependencies = [
+    "numpy>=1.13.3",
+    "pandas>=0.25.1",
+    "pooch>=1.4.0",
+    "chardet>=5.1.0",
+]
 
 [project.urls]
 Homepage = "https://fastlmm.github.io"