bed-reader 0.2.35__tar.gz → 0.2.37__tar.gz
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- bed_reader-0.2.37/.github/workflows/ci.yml +193 -0
- {bed_reader-0.2.35 → bed_reader-0.2.37}/Cargo.lock +25 -24
- {bed_reader-0.2.35 → bed_reader-0.2.37}/Cargo.toml +11 -5
- {bed_reader-0.2.35 → bed_reader-0.2.37}/PKG-INFO +4 -4
- {bed_reader-0.2.35 → bed_reader-0.2.37}/bed_reader/_open_bed.py +1 -1
- {bed_reader-0.2.35 → bed_reader-0.2.37}/pyproject.toml +7 -2
- bed_reader-0.2.37/tests/tests_api.rs +2248 -0
- {bed_reader-0.2.35 → bed_reader-0.2.37}/useful.bat +1 -1
- bed_reader-0.2.35/.github/workflows/ci.yml +0 -137
- bed_reader-0.2.35/bed_reader-0.2.35-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl +0 -0
- {bed_reader-0.2.35 → bed_reader-0.2.37}/.flake8 +0 -0
- {bed_reader-0.2.35 → bed_reader-0.2.37}/.gitignore +0 -0
- {bed_reader-0.2.35 → bed_reader-0.2.37}/.isort.cfg +0 -0
- {bed_reader-0.2.35 → bed_reader-0.2.37}/AUTHORS.txt +0 -0
- {bed_reader-0.2.35 → bed_reader-0.2.37}/LICENSE.md +0 -0
- {bed_reader-0.2.35 → bed_reader-0.2.37}/README-rust.md +0 -0
- {bed_reader-0.2.35 → bed_reader-0.2.37}/README.md +0 -0
- {bed_reader-0.2.35 → bed_reader-0.2.37}/bed_reader/__init__.py +0 -0
- {bed_reader-0.2.35 → bed_reader-0.2.37}/bed_reader/_sample_data.py +0 -0
- {bed_reader-0.2.35 → bed_reader-0.2.37}/bed_reader/_to_bed.py +0 -0
- {bed_reader-0.2.35 → bed_reader-0.2.37}/bed_reader/tests/__init__.py +0 -0
- {bed_reader-0.2.35 → bed_reader-0.2.37}/bed_reader/tests/benchmark/benchmark.py +0 -0
- {bed_reader-0.2.35 → bed_reader-0.2.37}/bed_reader/tests/data/500x400_o640_array.memmap +0 -0
- {bed_reader-0.2.35 → bed_reader-0.2.37}/bed_reader/tests/data/badfile.bed +0 -0
- {bed_reader-0.2.35 → bed_reader-0.2.37}/bed_reader/tests/data/empty.bed +0 -0
- {bed_reader-0.2.35 → bed_reader-0.2.37}/bed_reader/tests/data/plink_sim_10s_100v_10pmiss.bed +0 -0
- {bed_reader-0.2.35 → bed_reader-0.2.37}/bed_reader/tests/data/plink_sim_10s_100v_10pmiss.bim +0 -0
- {bed_reader-0.2.35 → bed_reader-0.2.37}/bed_reader/tests/data/plink_sim_10s_100v_10pmiss.fam +0 -0
- {bed_reader-0.2.35 → bed_reader-0.2.37}/bed_reader/tests/data/small.bad_bim +0 -0
- {bed_reader-0.2.35 → bed_reader-0.2.37}/bed_reader/tests/data/small.bed +0 -0
- {bed_reader-0.2.35 → bed_reader-0.2.37}/bed_reader/tests/data/small.bim +0 -0
- {bed_reader-0.2.35 → bed_reader-0.2.37}/bed_reader/tests/data/small.bim_bad_positions.bim +0 -0
- {bed_reader-0.2.35 → bed_reader-0.2.37}/bed_reader/tests/data/small.deb +0 -0
- {bed_reader-0.2.35 → bed_reader-0.2.37}/bed_reader/tests/data/small.fam +0 -0
- {bed_reader-0.2.35 → bed_reader-0.2.37}/bed_reader/tests/data/small.fam_bad +0 -0
- {bed_reader-0.2.35 → bed_reader-0.2.37}/bed_reader/tests/data/small.maf +0 -0
- {bed_reader-0.2.35 → bed_reader-0.2.37}/bed_reader/tests/data/small.mib +0 -0
- {bed_reader-0.2.35 → bed_reader-0.2.37}/bed_reader/tests/data/small2_array.memmap +0 -0
- {bed_reader-0.2.35 → bed_reader-0.2.37}/bed_reader/tests/data/small_array.memmap +0 -0
- {bed_reader-0.2.35 → bed_reader-0.2.37}/bed_reader/tests/data/small_no_bim.bed +0 -0
- {bed_reader-0.2.35 → bed_reader-0.2.37}/bed_reader/tests/data/small_no_bim.fam +0 -0
- {bed_reader-0.2.35 → bed_reader-0.2.37}/bed_reader/tests/data/small_no_fam.bed +0 -0
- {bed_reader-0.2.35 → bed_reader-0.2.37}/bed_reader/tests/data/small_no_fam.bim +0 -0
- {bed_reader-0.2.35 → bed_reader-0.2.37}/bed_reader/tests/data/small_too_short.bed +0 -0
- {bed_reader-0.2.35 → bed_reader-0.2.37}/bed_reader/tests/data/small_too_short.bim +0 -0
- {bed_reader-0.2.35 → bed_reader-0.2.37}/bed_reader/tests/data/small_too_short.fam +0 -0
- {bed_reader-0.2.35 → bed_reader-0.2.37}/bed_reader/tests/data/smallmode0.bed +0 -0
- {bed_reader-0.2.35 → bed_reader-0.2.37}/bed_reader/tests/data/smallmode0.bim +0 -0
- {bed_reader-0.2.35 → bed_reader-0.2.37}/bed_reader/tests/data/smallmode0.fam +0 -0
- {bed_reader-0.2.35 → bed_reader-0.2.37}/bed_reader/tests/data/smallmodebad.bed +0 -0
- {bed_reader-0.2.35 → bed_reader-0.2.37}/bed_reader/tests/data/some_missing.bed +0 -0
- {bed_reader-0.2.35 → bed_reader-0.2.37}/bed_reader/tests/data/some_missing.bim +0 -0
- {bed_reader-0.2.35 → bed_reader-0.2.37}/bed_reader/tests/data/some_missing.fam +0 -0
- {bed_reader-0.2.35 → bed_reader-0.2.37}/bed_reader/tests/data/some_missing.properties.npz +0 -0
- {bed_reader-0.2.35 → bed_reader-0.2.37}/bed_reader/tests/data/some_missing.val.npy +0 -0
- {bed_reader-0.2.35 → bed_reader-0.2.37}/bed_reader/tests/data/toydata.5chrom.bed +0 -0
- {bed_reader-0.2.35 → bed_reader-0.2.37}/bed_reader/tests/data/toydata.5chrom.bim +0 -0
- {bed_reader-0.2.35 → bed_reader-0.2.37}/bed_reader/tests/data/toydata.5chrom.fam +0 -0
- {bed_reader-0.2.35 → bed_reader-0.2.37}/bed_reader/tests/registry.txt +0 -0
- {bed_reader-0.2.35 → bed_reader-0.2.37}/bed_reader/tests/test_file_dot.py +0 -0
- {bed_reader-0.2.35 → bed_reader-0.2.37}/bed_reader/tests/test_open_bed.py +0 -0
- {bed_reader-0.2.35 → bed_reader-0.2.37}/build.rs +0 -0
- {bed_reader-0.2.35 → bed_reader-0.2.37}/pytest.ini +0 -0
- {bed_reader-0.2.35 → bed_reader-0.2.37}/requirements-dev.txt +0 -0
- {bed_reader-0.2.35 → bed_reader-0.2.37}/requirements.txt +0 -0
- {bed_reader-0.2.35 → bed_reader-0.2.37}/src/lib.rs +0 -0
- {bed_reader-0.2.35 → bed_reader-0.2.37}/src/python_module.rs +0 -0
- {bed_reader-0.2.35 → bed_reader-0.2.37}/src/tests.rs +0 -0
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@@ -1,19 +1,25 @@
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# See more keys and their definitions at https://doc.rust-lang.org/cargo/reference/manifest.html
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[package]
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version = "0.2.
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name = "bed-reader"
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description = "Read and write the PLINK BED format, simply and efficiently."
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documentation = "https://docs.rs/bed-reader/latest/bed_reader/"
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exclude = ["tests/*", "doc/*", "docs/*"]
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license = "Apache-2.0"
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keywords = ["bioinformatics", "plink", "genomics", "genotype", "snps"]
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categories = ["science"]
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edition = "2021"
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[lib]
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@@ -31,12 +37,12 @@ thiserror = "1.0.40"
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ndarray-npy = { version = "0.8.1", default-features = false }
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dpc-pariter = "0.4.0" # // pariter = "0.5.1"
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derive_builder = "0.12.0"
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|
temp_testdir = "0.2.3"
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|
@@ -52,4 +58,4 @@ fetch-data = "0.1.6"
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ndarray-rand = "0.14.0"
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[build-dependencies]
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|
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pyo3-build-config = "0.
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@@ -1,11 +1,11 @@
|
|
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Metadata-Version: 2.1
|
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Name: bed-reader
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|
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Version: 0.2.
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|
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Classifier: Programming Language :: Python :: 3.7
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Version: 0.2.37
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Classifier: Programming Language :: Python :: 3.8
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Classifier: Programming Language :: Python :: 3.9
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Classifier: Programming Language :: Python :: 3.10
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Classifier: Programming Language :: Python :: 3.11
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Classifier: Programming Language :: Python :: 3.12
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Classifier: Programming Language :: Python :: 3
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Classifier: Programming Language :: Python
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Requires-Dist: numpy>=1.13.3
|
|
@@ -22,9 +22,9 @@ Author-email: FaST-LMM Team <fastlmm-dev@python.org>
|
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License: Apache-2.0
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Description-Content-Type: text/markdown; charset=UTF-8; variant=GFM
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Project-URL: Source Code, https://github.com/fastlmm/bed-reader
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|
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Project-URL: Documentation, http://fastlmm.github.io/bed-reader
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|
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Project-URL: Bug Tracker, https://github.com/fastlmm/bed-reader/issues
|
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|
Project-URL: Homepage, https://fastlmm.github.io
|
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|
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Project-URL: Bug Tracker, https://github.com/fastlmm/bed-reader/issues
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Project-URL: Documentation, http://fastlmm.github.io/bed-reader
|
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[](https://badge.fury.io/py/bed-reader)
|
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|
|
@@ -39,7 +39,7 @@ def _sequence(key, length, missing, dtype):
|
|
|
39
39
|
longest = len(f"{key}{length}")
|
|
40
40
|
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|
|
41
41
|
return np.fromiter(
|
|
42
|
-
(f"{key}{i+1}" for i in range(length)), dtype=dtype, count=length
|
|
42
|
+
(f"{key}{i + 1}" for i in range(length)), dtype=dtype, count=length
|
|
43
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|
)
|
|
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|
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|
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|
@@ -2,15 +2,20 @@
|
|
|
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2
|
name = "bed-reader"
|
|
3
3
|
readme = "README.md"
|
|
4
4
|
classifiers = [
|
|
5
|
-
"Programming Language :: Python :: 3.7",
|
|
6
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|
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|
|
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|
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|
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|
"Programming Language :: Python :: 3.10",
|
|
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|
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|
|
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|
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|
|
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|
"Programming Language :: Python :: 3",
|
|
11
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|
"Programming Language :: Python",
|
|
12
12
|
]
|
|
13
|
-
dependencies = [
|
|
13
|
+
dependencies = [
|
|
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|
+
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|
|
15
|
+
"pandas>=0.25.1",
|
|
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|
+
"pooch>=1.4.0",
|
|
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|
+
"chardet>=5.1.0",
|
|
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|
+
]
|
|
14
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|
|
|
15
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|
[project.urls]
|
|
16
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|
Homepage = "https://fastlmm.github.io"
|