bed-reader 1.0.6__tar.gz → 1.0.6a1__tar.gz

{bed_reader-1.0.6 → bed_reader-1.0.6a1}/.github/workflows/ci.yml

@@ -26,17 +26,23 @@ jobs:
     runs-on: ${{ matrix.os }}
     steps:
       - name: Checkout
-        uses: actions/checkout@v4
-      - name: Set up Rust (Pinned Version)
-        uses: dtolnay/rust-toolchain@1.81.0
+        uses: actions/checkout@v3
+      - name: Set up Rust
+        uses: actions-rs/toolchain@v1
         with:
-          components: clippy, rustfmt, rust-src
+          toolchain: 1.81
+          override: true
+      - name: Install Clippy (pinned version for this pinned version of Rust)
+        run: rustup component add clippy
       - name: Run Clippy (strict for this pinned version of Rust)
         run: cargo clippy --all-targets --all-features -- -D warnings
-      - name: Set up Rust (Latest Stable)
-        uses: dtolnay/rust-toolchain@stable
+      - name: Set up Rust (Latest Stable for Tests)
+        uses: actions-rs/toolchain@v1
         with:
-          components: clippy, rustfmt, rust-src
+          toolchain: stable
+          override: true
+      - name: Install Clippy (Latest)
+        run: rustup component add clippy
       - name: Run Clippy (lenient for latest version)
         run: cargo clippy --all-targets --all-features -- -A warnings || echo "Clippy warnings from the latest version"
       - name: Test Rust no-default-features
@@ -177,29 +183,27 @@ jobs:
       uses: astral-sh/setup-uv@v3
     - name: Install Python ${{ matrix.python-version }}
       run: uv python install ${{ matrix.python-version }}
-    - name: Pinned Ruff
-      run:  uvx ruff@0.6.9 check bed_reader
-    - name: Lastest Ruff (just to check for warnings)
-      run: uvx ruff@latest check bed_reader || echo "Ignoring warnings from the latest version of ruff"
-    - name: Install minimal dependencies
-      run: uv sync --extra min_dev
-    - name: Run min tests
-      shell: bash
+    - name: Setup, Lint, and Test Python (Linux/macOS)
+      if: runner.os != 'Windows'
       run: |
-        if [[ "$RUNNER_OS" != "Windows" ]]; then
-          source .venv/bin/activate
-        else
-          source .venv/Scripts/activate
-        fi
-        pytest bed_reader/tests/test_opt_dep.py  
-    - name: Install all dependencies
-      run: uv sync --all-extras
-    - name: Run all tests
-      shell: bash
-      run: |
-        if [[ "$RUNNER_OS" != "Windows" ]]; then
-          source .venv/bin/activate
-        else
-          source .venv/Scripts/activate
-        fi
+        cd bed_reader
+        uvx ruff@0.6.9 check .
+        uvx ruff@latest check . || echo "Ignoring warnings from the latest version of ruff"
+        uv sync --extra min_dev
+        source ../.venv/bin/activate
+        pytest tests/test_opt_dep.py
+        uv sync --extra dev --extra sparse --extra samples
+        source ../.venv/bin/activate
         pytest .
+    - name: Setup, Lint, and Test Python (Windows)
+      if: runner.os == 'Windows'
+      run: |
+        cd bed_reader
+        uvx ruff@0.6.9 check .
+        uvx ruff@latest check . || echo "Ignoring warnings from the latest version of ruff"
+        uv sync --extra min_dev
+        ../.venv/Scripts/activate
+        pytest tests/test_opt_dep.py
+        uv sync --extra dev --extra sparse --extra samples
+        ../.venv/Scripts/activate
+        pytest .

{bed_reader-1.0.6 → bed_reader-1.0.6a1}/Cargo.lock

@@ -40,38 +40,38 @@ dependencies = [
 
 [[package]]
 name = "anyhow"
-version = "1.0.92"
+version = "1.0.89"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "74f37166d7d48a0284b99dd824694c26119c700b53bf0d1540cdb147dbdaaf13"
+checksum = "86fdf8605db99b54d3cd748a44c6d04df638eb5dafb219b135d0149bd0db01f6"
 
 [[package]]
 name = "anyinput"
-version = "0.1.8"
+version = "0.1.6"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "2258806477d4f8a19164f334195cb54ce8af7e7783a82125db278177819eb321"
+checksum = "c85db6a01ea7a4de03af7aeb994c0febc1f6c5e27b204c3c0817a3299f2805fd"
 dependencies = [
  "anyinput-derive",
 ]
 
 [[package]]
 name = "anyinput-core"
-version = "0.1.8"
+version = "0.1.6"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "49cf1db198c8a687ca9e640d8553690c1097c472e634808b3dbe83f97b30c79f"
+checksum = "16a3bb0de9bada3de586cea88206fa6760d669aa0e4b983713c437ebd5110aca"
 dependencies = [
- "ndarray",
+ "ndarray 0.15.6",
  "proc-macro-error",
  "proc-macro2",
  "quote",
  "strum",
- "syn 2.0.87",
+ "syn 1.0.109",
 ]
 
 [[package]]
 name = "anyinput-derive"
-version = "0.1.8"
+version = "0.1.6"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "fe54127313c239e27f8157caa3514373ab64af729085ec7bef08d6a9679b8ff5"
+checksum = "32bcdb4d47b8364f2a464ad7e7a15705e435cee8f8e462991491c0b7bfb505b9"
 dependencies = [
  "anyinput-core",
  "proc-macro-error",
@@ -95,7 +95,7 @@ checksum = "6e0c28dcc82d7c8ead5cb13beb15405b57b8546e93215673ff8ca0349a028107"
 dependencies = [
  "proc-macro2",
  "quote",
- "syn 2.0.87",
+ "syn 2.0.79",
 ]
 
 [[package]]
@@ -139,7 +139,7 @@ checksum = "72b3254f16251a8381aa12e40e3c4d2f0199f8c6508fbecb9d91f575e0fbb8c6"
 
 [[package]]
 name = "bed-reader"
-version = "1.0.6"
+version = "1.0.6-alpha.1"
 dependencies = [
  "anyhow",
  "anyinput",
@@ -152,7 +152,7 @@ dependencies = [
  "fetch-data",
  "futures-util",
  "itertools",
- "ndarray",
+ "ndarray 0.16.1",
  "ndarray-npy",
  "ndarray-rand",
  "num-traits",
@@ -209,9 +209,9 @@ checksum = "1fd0f2584146f6f2ef48085050886acf353beff7305ebd1ae69500e27c67f64b"
 
 [[package]]
 name = "bytes"
-version = "1.8.0"
+version = "1.7.2"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "9ac0150caa2ae65ca5bd83f25c7de183dea78d4d366469f148435e2acfbad0da"
+checksum = "428d9aa8fbc0670b7b8d6030a7fadd0f86151cae55e4dbbece15f3780a3dfaf3"
 
 [[package]]
 name = "cc"
@@ -364,7 +364,7 @@ source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "edb49164822f3ee45b17acd4a208cfc1251410cf0cad9a833234c9890774dd9f"
 dependencies = [
  "quote",
- "syn 2.0.87",
+ "syn 2.0.79",
 ]
 
 [[package]]
@@ -388,7 +388,7 @@ dependencies = [
  "proc-macro2",
  "quote",
  "strsim",
- "syn 2.0.87",
+ "syn 2.0.79",
 ]
 
 [[package]]
@@ -399,7 +399,7 @@ checksum = "d336a2a514f6ccccaa3e09b02d41d35330c07ddf03a62165fcec10bb561c7806"
 dependencies = [
  "darling_core",
  "quote",
- "syn 2.0.87",
+ "syn 2.0.79",
 ]
 
 [[package]]
@@ -420,7 +420,7 @@ dependencies = [
  "darling",
  "proc-macro2",
  "quote",
- "syn 2.0.87",
+ "syn 2.0.79",
 ]
 
 [[package]]
@@ -430,7 +430,7 @@ source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "ab63b0e2bf4d5928aff72e83a7dace85d7bba5fe12dcc3c5a572d78caffd3f3c"
 dependencies = [
  "derive_builder_core",
- "syn 2.0.87",
+ "syn 2.0.79",
 ]
 
 [[package]]
@@ -606,7 +606,7 @@ checksum = "162ee34ebcb7c64a8abebc059ce0fee27c2262618d7b60ed8faf72fef13c3650"
 dependencies = [
  "proc-macro2",
  "quote",
- "syn 2.0.87",
+ "syn 2.0.79",
 ]
 
 [[package]]
@@ -693,6 +693,12 @@ version = "0.15.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "1e087f84d4f86bf4b218b927129862374b72199ae7d8657835f1e89000eea4fb"
 
+[[package]]
+name = "heck"
+version = "0.4.1"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "95505c38b4572b2d910cecb0281560f54b440a19336cbbcb27bf6ce6adc6f5a8"
+
 [[package]]
 name = "heck"
 version = "0.5.0"
@@ -1079,7 +1085,20 @@ checksum = "254a5372af8fc138e36684761d3c0cdb758a4410e938babcff1c860ce14ddbfc"
 dependencies = [
  "proc-macro2",
  "quote",
- "syn 2.0.87",
+ "syn 2.0.79",
+]
+
+[[package]]
+name = "ndarray"
+version = "0.15.6"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "adb12d4e967ec485a5f71c6311fe28158e9d6f4bc4a447b474184d0f91a8fa32"
+dependencies = [
+ "matrixmultiply",
+ "num-complex",
+ "num-integer",
+ "num-traits",
+ "rawpointer",
 ]
 
 [[package]]
@@ -1106,7 +1125,7 @@ source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "7b313788c468c49141a9d9b6131fc15f403e6ef4e8446a0b2e18f664ddb278a9"
 dependencies = [
  "byteorder",
- "ndarray",
+ "ndarray 0.16.1",
  "num-traits",
  "py_literal",
 ]
@@ -1117,7 +1136,7 @@ version = "0.15.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "f093b3db6fd194718dcdeea6bd8c829417deae904e3fcc7732dabcd4416d25d8"
 dependencies = [
- "ndarray",
+ "ndarray 0.16.1",
  "rand",
  "rand_distr",
 ]
@@ -1182,12 +1201,12 @@ dependencies = [
 
 [[package]]
 name = "numpy"
-version = "0.22.1"
+version = "0.22.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "edb929bc0da91a4d85ed6c0a84deaa53d411abfb387fc271124f91bf6b89f14e"
+checksum = "cf314fca279e6e6ac2126a4ff98f26d88aa4ad06bc68fb6ae5cf4bd706758311"
 dependencies = [
  "libc",
- "ndarray",
+ "ndarray 0.16.1",
  "num-complex",
  "num-integer",
  "num-traits",
@@ -1319,7 +1338,7 @@ dependencies = [
  "pest_meta",
  "proc-macro2",
  "quote",
- "syn 2.0.87",
+ "syn 2.0.79",
 ]
 
 [[package]]
@@ -1462,7 +1481,7 @@ dependencies = [
  "proc-macro2",
  "pyo3-macros-backend",
  "quote",
- "syn 2.0.87",
+ "syn 2.0.79",
 ]
 
 [[package]]
@@ -1471,11 +1490,11 @@ version = "0.22.5"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "ae1e3f09eecd94618f60a455a23def79f79eba4dc561a97324bf9ac8c6df30ce"
 dependencies = [
- "heck",
+ "heck 0.5.0",
  "proc-macro2",
  "pyo3-build-config",
  "quote",
- "syn 2.0.87",
+ "syn 2.0.79",
 ]
 
 [[package]]
@@ -1866,7 +1885,7 @@ checksum = "243902eda00fad750862fc144cea25caca5e20d615af0a81bee94ca738f1df1f"
 dependencies = [
  "proc-macro2",
  "quote",
- "syn 2.0.87",
+ "syn 2.0.79",
 ]
 
 [[package]]
@@ -1962,10 +1981,10 @@ version = "0.8.5"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "03c3c6b7927ffe7ecaa769ee0e3994da3b8cafc8f444578982c83ecb161af917"
 dependencies = [
- "heck",
+ "heck 0.5.0",
  "proc-macro2",
  "quote",
- "syn 2.0.87",
+ "syn 2.0.79",
 ]
 
 [[package]]
@@ -2004,24 +2023,24 @@ checksum = "7da8b5736845d9f2fcb837ea5d9e2628564b3b043a70948a3f0b778838c5fb4f"
 
 [[package]]
 name = "strum"
-version = "0.26.3"
+version = "0.24.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "8fec0f0aef304996cf250b31b5a10dee7980c85da9d759361292b8bca5a18f06"
+checksum = "063e6045c0e62079840579a7e47a355ae92f60eb74daaf156fb1e84ba164e63f"
 dependencies = [
  "strum_macros",
 ]
 
 [[package]]
 name = "strum_macros"
-version = "0.26.4"
+version = "0.24.3"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "4c6bee85a5a24955dc440386795aa378cd9cf82acd5f764469152d2270e581be"
+checksum = "1e385be0d24f186b4ce2f9982191e7101bb737312ad61c1f2f984f34bcf85d59"
 dependencies = [
- "heck",
+ "heck 0.4.1",
  "proc-macro2",
  "quote",
  "rustversion",
- "syn 2.0.87",
+ "syn 1.0.109",
 ]
 
 [[package]]
@@ -2037,14 +2056,15 @@ source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "72b64191b275b66ffe2469e8af2c1cfe3bafa67b529ead792a6d0160888b4237"
 dependencies = [
  "proc-macro2",
+ "quote",
  "unicode-ident",
 ]
 
 [[package]]
 name = "syn"
-version = "2.0.87"
+version = "2.0.79"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "25aa4ce346d03a6dcd68dd8b4010bcb74e54e62c90c573f394c46eae99aba32d"
+checksum = "89132cd0bf050864e1d38dc3bbc07a0eb8e7530af26344d3d2bbbef83499f590"
 dependencies = [
  "proc-macro2",
  "quote",
@@ -2074,22 +2094,22 @@ checksum = "921f1e9c427802414907a48b21a6504ff6b3a15a1a3cf37e699590949ad9befc"
 
 [[package]]
 name = "thiserror"
-version = "1.0.66"
+version = "1.0.64"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "5d171f59dbaa811dbbb1aee1e73db92ec2b122911a48e1390dfe327a821ddede"
+checksum = "d50af8abc119fb8bb6dbabcfa89656f46f84aa0ac7688088608076ad2b459a84"
 dependencies = [
  "thiserror-impl",
 ]
 
 [[package]]
 name = "thiserror-impl"
-version = "1.0.66"
+version = "1.0.64"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "b08be0f17bd307950653ce45db00cd31200d82b624b36e181337d9c7d92765b5"
+checksum = "08904e7672f5eb876eaaf87e0ce17857500934f4981c4a0ab2b4aa98baac7fc3"
 dependencies = [
  "proc-macro2",
  "quote",
- "syn 2.0.87",
+ "syn 2.0.79",
 ]
 
 [[package]]
@@ -2115,9 +2135,9 @@ checksum = "1f3ccbac311fea05f86f61904b462b55fb3df8837a366dfc601a0161d0532f20"
 
 [[package]]
 name = "tokio"
-version = "1.41.0"
+version = "1.40.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "145f3413504347a2be84393cc8a7d2fb4d863b375909ea59f2158261aa258bbb"
+checksum = "e2b070231665d27ad9ec9b8df639893f46727666c6767db40317fbe920a5d998"
 dependencies = [
  "backtrace",
  "bytes",
@@ -2139,7 +2159,7 @@ checksum = "693d596312e88961bc67d7f1f97af8a70227d9f90c31bba5806eec004978d752"
 dependencies = [
  "proc-macro2",
  "quote",
- "syn 2.0.87",
+ "syn 2.0.79",
 ]
 
 [[package]]
@@ -2191,7 +2211,7 @@ checksum = "34704c8d6ebcbc939824180af020566b01a7c01f80641264eba0999f6c2b6be7"
 dependencies = [
  "proc-macro2",
  "quote",
- "syn 2.0.87",
+ "syn 2.0.79",
 ]
 
 [[package]]
@@ -2334,7 +2354,7 @@ dependencies = [
  "once_cell",
  "proc-macro2",
  "quote",
- "syn 2.0.87",
+ "syn 2.0.79",
  "wasm-bindgen-shared",
 ]
 
@@ -2368,7 +2388,7 @@ checksum = "26c6ab57572f7a24a4985830b120de1594465e5d500f24afe89e16b4e833ef68"
 dependencies = [
  "proc-macro2",
  "quote",
- "syn 2.0.87",
+ "syn 2.0.79",
  "wasm-bindgen-backend",
  "wasm-bindgen-shared",
 ]
@@ -2657,7 +2677,7 @@ checksum = "fa4f8080344d4671fb4e831a13ad1e68092748387dfc4f55e356242fae12ce3e"
 dependencies = [
  "proc-macro2",
  "quote",
- "syn 2.0.87",
+ "syn 2.0.79",
 ]
 
 [[package]]

{bed_reader-1.0.6 → bed_reader-1.0.6a1}/Cargo.toml

@@ -1,5 +1,5 @@
 [package]
-version = "1.0.6"
+version = "1.0.6-alpha.1"
 name = "bed-reader"
 description = "Read and write the PLINK BED format, simply and efficiently."
 repository = "https://github.com/fastlmm/bed-reader"
@@ -33,29 +33,29 @@ tokio = ["dep:tokio"]
 extension-module = ["pyo3/extension-module", "tokio"]
 
 [dependencies]
-thiserror = "1.0.66"
+thiserror = "1.0.64"
 num-traits = "0.2.19"
 ndarray-npy = { version = "0.9.1", default-features = false }
 rayon = "1.10.0"
-numpy = "0.22.1"
+numpy = "0.22.0"
 ndarray = { version = "0.16.1", features = ["approx", "rayon"] }
 statrs = "0.17.1"
 byteorder = { version = "1.5.0", default-features = false }
 dpc-pariter = "0.4.0"                                                           # //  pariter = "0.5.1"
 derive_builder = "0.20.2"
-anyinput = { version = "0.1.8", features = ["ndarray"] }
+anyinput = { version = "0.1.6", features = ["ndarray"] }
 fetch-data = "0.2.0"
 futures-util = { version = "0.3.31" }
 bytecount = { version = "0.6.8" }
 itertools = { version = "0.13.0" }
-bytes = { version = "1.8.0" }
+bytes = { version = "1.7.2" }
 cloud-file = { version = "0.2.0" }
 pyo3 = { version = "0.22.5", features = ["extension-module"], optional = true }
-tokio = { version = "1.41.0", features = ["full"], optional = true }
+tokio = { version = "1.40.0", features = ["full"], optional = true }
 
 [dev-dependencies]
 ndarray-rand = "0.15.0"
-anyhow = "1.0.92"
+anyhow = "1.0.89"
 rusoto_credential = "0.48.0"
 temp_testdir = "0.2.3"
 thousands = "0.2.0"

{bed_reader-1.0.6 → bed_reader-1.0.6a1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: bed-reader
-Version: 1.0.6
+Version: 1.0.6a1
 Classifier: Programming Language :: Python
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11