From 0fa5f4f03183bec97f6f06a0a46369b6e4db4254 Mon Sep 17 00:00:00 2001
From: Arya Massarat <23412689+aryarm@users.noreply.github.com>
Date: Sat, 5 Nov 2022 21:43:03 -0700
Subject: [PATCH 01/10] update install docs with quoting

---
 docs/project_info/installation.rst | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/docs/project_info/installation.rst b/docs/project_info/installation.rst
index f8794189..f6da301a 100644
--- a/docs/project_info/installation.rst
+++ b/docs/project_info/installation.rst
@@ -17,7 +17,7 @@ Installing ``haptools`` with the "files" extra requirements enables automatic su
 
 .. code-block:: bash
 
-   pip install haptools[files]
+   pip install 'haptools[files]'
 
 .. note::
    Installing ``haptools`` with the "files" extra requirement requires ``gcc`` and a few other compiler tools. Please make sure that they are installed first. To install with conda, for example, please execute the following:
@@ -37,7 +37,7 @@ Installing ``haptools`` with the "files" extra requirements enables automatic su
 Using conda
 -----------
 
-We also support installing ``haptools`` from bioconda.
+We also support installing ``haptools`` from bioconda using ``conda``.
 
 .. code-block:: bash
 

From 8411f3c2681c437b79fa7f257d76c0c1704b9879 Mon Sep 17 00:00:00 2001
From: Arya Massarat <23412689+aryarm@users.noreply.github.com>
Date: Sat, 5 Nov 2022 21:43:20 -0700
Subject: [PATCH 02/10] lock pysam at v0.19.0 it's the easiest version to
 install b/c 0.19.1 has no wheels and 0.20.0 has no sdist

---
 poetry.lock | 107 ++++++++++++++++++++++++++--------------------------
 1 file changed, 54 insertions(+), 53 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index fc585454..579d1045 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -23,10 +23,10 @@ optional = false
 python-versions = ">=3.5"
 
 [package.extras]
-dev = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "mypy (>=0.900,!=0.940)", "pytest-mypy-plugins", "zope.interface", "furo", "sphinx", "sphinx-notfound-page", "pre-commit", "cloudpickle"]
-docs = ["furo", "sphinx", "zope.interface", "sphinx-notfound-page"]
-tests = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "mypy (>=0.900,!=0.940)", "pytest-mypy-plugins", "zope.interface", "cloudpickle"]
-tests_no_zope = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "mypy (>=0.900,!=0.940)", "pytest-mypy-plugins", "cloudpickle"]
+dev = ["cloudpickle", "coverage[toml] (>=5.0.2)", "furo", "hypothesis", "mypy (>=0.900,!=0.940)", "pre-commit", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "sphinx", "sphinx-notfound-page", "zope.interface"]
+docs = ["furo", "sphinx", "sphinx-notfound-page", "zope.interface"]
+tests = ["cloudpickle", "coverage[toml] (>=5.0.2)", "hypothesis", "mypy (>=0.900,!=0.940)", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "zope.interface"]
+tests_no_zope = ["cloudpickle", "coverage[toml] (>=5.0.2)", "hypothesis", "mypy (>=0.900,!=0.940)", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins"]
 
 [[package]]
 name = "babel"
@@ -180,9 +180,9 @@ optional = false
 python-versions = ">=3.7"
 
 [package.extras]
-all = ["fs (>=2.2.0,<3)", "lxml (>=4.0,<5)", "zopfli (>=0.1.4)", "lz4 (>=1.7.4.2)", "matplotlib", "sympy", "skia-pathops (>=0.5.0)", "uharfbuzz (>=0.23.0)", "brotlicffi (>=0.8.0)", "scipy", "brotli (>=1.0.1)", "munkres", "unicodedata2 (>=14.0.0)", "xattr"]
+all = ["brotli (>=1.0.1)", "brotlicffi (>=0.8.0)", "fs (>=2.2.0,<3)", "lxml (>=4.0,<5)", "lz4 (>=1.7.4.2)", "matplotlib", "munkres", "scipy", "skia-pathops (>=0.5.0)", "sympy", "uharfbuzz (>=0.23.0)", "unicodedata2 (>=14.0.0)", "xattr", "zopfli (>=0.1.4)"]
 graphite = ["lz4 (>=1.7.4.2)"]
-interpolatable = ["scipy", "munkres"]
+interpolatable = ["munkres", "scipy"]
 lxml = ["lxml (>=4.0,<5)"]
 pathops = ["skia-pathops (>=0.5.0)"]
 plot = ["matplotlib"]
@@ -191,7 +191,7 @@ symfont = ["sympy"]
 type1 = ["xattr"]
 ufo = ["fs (>=2.2.0,<3)"]
 unicode = ["unicodedata2 (>=14.0.0)"]
-woff = ["zopfli (>=0.1.4)", "brotlicffi (>=0.8.0)", "brotli (>=1.0.1)"]
+woff = ["brotli (>=1.0.1)", "brotlicffi (>=0.8.0)", "zopfli (>=0.1.4)"]
 
 [[package]]
 name = "humanfriendly"
@@ -234,9 +234,9 @@ typing-extensions = {version = ">=3.6.4", markers = "python_version < \"3.8\""}
 zipp = ">=0.5"
 
 [package.extras]
-docs = ["sphinx (>=3.5)", "jaraco.packaging (>=9)", "rst.linker (>=1.9)", "furo", "jaraco.tidelift (>=1.4)"]
+docs = ["furo", "jaraco.packaging (>=9)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)"]
 perf = ["ipython"]
-testing = ["pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-flake8", "flake8 (<5)", "pytest-cov", "pytest-enabler (>=1.3)", "packaging", "pyfakefs", "flufl.flake8", "pytest-perf (>=0.9.2)", "pytest-black (>=0.3.7)", "pytest-mypy (>=0.9.1)", "importlib-resources (>=1.3)"]
+testing = ["flake8 (<5)", "flufl.flake8", "importlib-resources (>=1.3)", "packaging", "pyfakefs", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=1.3)", "pytest-flake8", "pytest-mypy (>=0.9.1)", "pytest-perf (>=0.9.2)"]
 
 [[package]]
 name = "iniconfig"
@@ -273,10 +273,10 @@ doc = ["Sphinx (>=1.3)"]
 kernel = ["ipykernel"]
 nbconvert = ["nbconvert"]
 nbformat = ["nbformat"]
-notebook = ["notebook", "ipywidgets"]
+notebook = ["ipywidgets", "notebook"]
 parallel = ["ipyparallel"]
 qtconsole = ["qtconsole"]
-test = ["nose (>=0.10.1)", "requests", "testpath", "pygments", "nbformat", "ipykernel", "numpy (>=1.17)"]
+test = ["ipykernel", "nbformat", "nose (>=0.10.1)", "numpy (>=1.17)", "pygments", "requests", "testpath"]
 
 [[package]]
 name = "jedi"
@@ -385,7 +385,7 @@ Jinja2 = ">=2.10"
 sphinx = ">=4.2"
 
 [package.extras]
-testing = ["pytest", "pytest-cov", "matplotlib"]
+testing = ["matplotlib", "pytest", "pytest-cov"]
 
 [[package]]
 name = "packaging"
@@ -466,8 +466,8 @@ optional = false
 python-versions = ">=3.7"
 
 [package.extras]
-docs = ["furo (>=2021.7.5b38)", "proselint (>=0.10.2)", "sphinx-autodoc-typehints (>=1.12)", "sphinx (>=4)"]
-test = ["appdirs (==1.4.4)", "pytest-cov (>=2.7)", "pytest-mock (>=3.6)", "pytest (>=6)"]
+docs = ["furo (>=2021.7.5b38)", "proselint (>=0.10.2)", "sphinx (>=4)", "sphinx-autodoc-typehints (>=1.12)"]
+test = ["appdirs (==1.4.4)", "pytest (>=6)", "pytest-cov (>=2.7)", "pytest-mock (>=3.6)"]
 
 [[package]]
 name = "pluggy"
@@ -523,7 +523,7 @@ optional = false
 python-versions = ">=3.6.8"
 
 [package.extras]
-diagrams = ["railroad-diagrams", "jinja2"]
+diagrams = ["jinja2", "railroad-diagrams"]
 
 [[package]]
 name = "pyreadline"
@@ -543,7 +543,7 @@ python-versions = "*"
 
 [[package]]
 name = "pysam"
-version = "0.20.0"
+version = "0.19.0"
 description = "pysam"
 category = "main"
 optional = false
@@ -668,8 +668,8 @@ sphinxcontrib-serializinghtml = ">=1.1.5"
 
 [package.extras]
 docs = ["sphinxcontrib-websupport"]
-lint = ["flake8 (>=3.5.0)", "flake8-comprehensions", "flake8-bugbear", "flake8-simplify", "isort", "mypy (>=0.981)", "sphinx-lint", "docutils-stubs", "types-typed-ast", "types-requests"]
-test = ["pytest (>=4.6)", "html5lib", "typed-ast", "cython"]
+lint = ["docutils-stubs", "flake8 (>=3.5.0)", "flake8-bugbear", "flake8-comprehensions", "flake8-simplify", "isort", "mypy (>=0.981)", "sphinx-lint", "types-requests", "types-typed-ast"]
+test = ["cython", "html5lib", "pytest (>=4.6)", "typed-ast"]
 
 [[package]]
 name = "sphinx-autodoc-typehints"
@@ -683,8 +683,8 @@ python-versions = ">=3.7"
 sphinx = ">=5.3"
 
 [package.extras]
-docs = ["furo (>=2022.9.29)", "sphinx-autodoc-typehints (>=1.19.4)", "sphinx (>=5.3)"]
-testing = ["covdefaults (>=2.2)", "coverage (>=6.5)", "diff-cover (>=7.0.1)", "nptyping (>=2.3.1)", "pytest-cov (>=4)", "pytest (>=7.2)", "sphobjinv (>=2.2.2)", "typing-extensions (>=4.4)"]
+docs = ["furo (>=2022.9.29)", "sphinx (>=5.3)", "sphinx-autodoc-typehints (>=1.19.4)"]
+testing = ["covdefaults (>=2.2)", "coverage (>=6.5)", "diff-cover (>=7.0.1)", "nptyping (>=2.3.1)", "pytest (>=7.2)", "pytest-cov (>=4)", "sphobjinv (>=2.2.2)", "typing-extensions (>=4.4)"]
 type-comment = ["typed-ast (>=1.5.4)"]
 
 [[package]]
@@ -713,7 +713,7 @@ docutils = "<0.18"
 sphinx = ">=1.6,<6"
 
 [package.extras]
-dev = ["transifex-client", "sphinxcontrib-httpdomain", "bump2version", "wheel"]
+dev = ["bump2version", "sphinxcontrib-httpdomain", "transifex-client", "wheel"]
 
 [[package]]
 name = "sphinxcontrib-applehelp"
@@ -724,7 +724,7 @@ optional = false
 python-versions = ">=3.5"
 
 [package.extras]
-lint = ["flake8", "mypy", "docutils-stubs"]
+lint = ["docutils-stubs", "flake8", "mypy"]
 test = ["pytest"]
 
 [[package]]
@@ -736,7 +736,7 @@ optional = false
 python-versions = ">=3.5"
 
 [package.extras]
-lint = ["flake8", "mypy", "docutils-stubs"]
+lint = ["docutils-stubs", "flake8", "mypy"]
 test = ["pytest"]
 
 [[package]]
@@ -748,8 +748,8 @@ optional = false
 python-versions = ">=3.6"
 
 [package.extras]
-lint = ["flake8", "mypy", "docutils-stubs"]
-test = ["pytest", "html5lib"]
+lint = ["docutils-stubs", "flake8", "mypy"]
+test = ["html5lib", "pytest"]
 
 [[package]]
 name = "sphinxcontrib-jsmath"
@@ -760,7 +760,7 @@ optional = false
 python-versions = ">=3.5"
 
 [package.extras]
-test = ["pytest", "flake8", "mypy"]
+test = ["flake8", "mypy", "pytest"]
 
 [[package]]
 name = "sphinxcontrib-qthelp"
@@ -771,7 +771,7 @@ optional = false
 python-versions = ">=3.5"
 
 [package.extras]
-lint = ["flake8", "mypy", "docutils-stubs"]
+lint = ["docutils-stubs", "flake8", "mypy"]
 test = ["pytest"]
 
 [[package]]
@@ -783,7 +783,7 @@ optional = false
 python-versions = ">=3.5"
 
 [package.extras]
-lint = ["flake8", "mypy", "docutils-stubs"]
+lint = ["docutils-stubs", "flake8", "mypy"]
 test = ["pytest"]
 
 [[package]]
@@ -831,8 +831,8 @@ optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*, <4"
 
 [package.extras]
-brotli = ["brotlicffi (>=0.8.0)", "brotli (>=1.0.9)", "brotlipy (>=0.6.0)"]
-secure = ["pyOpenSSL (>=0.14)", "cryptography (>=1.3.4)", "idna (>=2.0.0)", "certifi", "urllib3-secure-extra", "ipaddress"]
+brotli = ["brotli (>=1.0.9)", "brotlicffi (>=0.8.0)", "brotlipy (>=0.6.0)"]
+secure = ["certifi", "cryptography (>=1.3.4)", "idna (>=2.0.0)", "ipaddress", "pyOpenSSL (>=0.14)", "urllib3-secure-extra"]
 socks = ["PySocks (>=1.5.6,!=1.5.7,<2.0)"]
 
 [[package]]
@@ -852,8 +852,8 @@ optional = false
 python-versions = ">=3.7"
 
 [package.extras]
-docs = ["sphinx (>=3.5)", "jaraco.packaging (>=9)", "rst.linker (>=1.9)", "furo", "jaraco.tidelift (>=1.4)"]
-testing = ["pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-flake8", "flake8 (<5)", "pytest-cov", "pytest-enabler (>=1.3)", "jaraco.itertools", "func-timeout", "jaraco.functools", "more-itertools", "pytest-black (>=0.3.7)", "pytest-mypy (>=0.9.1)"]
+docs = ["furo", "jaraco.packaging (>=9)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)"]
+testing = ["flake8 (<5)", "func-timeout", "jaraco.functools", "jaraco.itertools", "more-itertools", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=1.3)", "pytest-flake8", "pytest-mypy (>=0.9.1)"]
 
 [extras]
 docs = ["Sphinx", "sphinx-autodoc-typehints", "sphinx-rtd-theme", "numpydoc", "sphinx-click"]
@@ -863,7 +863,7 @@ test = []
 [metadata]
 lock-version = "1.1"
 python-versions = ">=3.7,<3.11"
-content-hash = "64aa23c3ce4ed3e5a98d911b753ca01d33fbb01eb76a417d0e25adc5f82918a3"
+content-hash = "196d5c25fdf05c7f9356c71e7c851cf3b4abd58101ba0eb6e6db7d0d60ca0708"
 
 [metadata.files]
 alabaster = [
@@ -1312,26 +1312,27 @@ pyreadline3 = [
     {file = "pyreadline3-3.4.1.tar.gz", hash = "sha256:6f3d1f7b8a31ba32b73917cefc1f28cc660562f39aea8646d30bd6eff21f7bae"},
 ]
 pysam = [
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+    {file = "pysam-0.19.0-cp37-cp37m-manylinux_2_12_x86_64.manylinux2010_x86_64.whl", hash = "sha256:80b8f5b929c7f660b6e1497790a13c61f386b310a31ca54ad6ba110674d11c55"},
+    {file = "pysam-0.19.0-cp37-cp37m-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:30017bed8d002d41f83fa7e10569525c811a8e3860d73a880ee653ef29fd4fbc"},
+    {file = "pysam-0.19.0-cp38-cp38-macosx_10_9_x86_64.whl", hash = "sha256:5e2e465522ba2c34cb96c013a28f9c9db303f8ab1350b4c11cca73677f1e9594"},
+    {file = "pysam-0.19.0-cp38-cp38-manylinux_2_12_i686.manylinux2010_i686.whl", hash = "sha256:2103b4b6d9b0cc0b4aaccf64e87a92bfdabb7dc92810cf84be35ffe78fafa002"},
+    {file = "pysam-0.19.0-cp38-cp38-manylinux_2_12_x86_64.manylinux2010_x86_64.whl", hash = "sha256:eaf342b9c71ed83a63237df2000e3bc1f0236165d48fd7240c4c78b66f28d63b"},
+    {file = "pysam-0.19.0-cp38-cp38-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:bc0021b154206edfbaa13515cb67523c76c576b7a670e72a793f2da4f03139f4"},
+    {file = "pysam-0.19.0-cp39-cp39-macosx_10_9_x86_64.whl", hash = "sha256:3101e0fcd2f6accbfa72a554a71baf83f1c096bb0f9045059b3ead35901ce128"},
+    {file = "pysam-0.19.0-cp39-cp39-manylinux_2_12_i686.manylinux2010_i686.whl", hash = "sha256:5118dcabac574638df43739941f0ee20cc4e9197aee4a8f10f195542a13f18e3"},
+    {file = "pysam-0.19.0-cp39-cp39-manylinux_2_12_x86_64.manylinux2010_x86_64.whl", hash = "sha256:4fe1f1fae0e559d3412625dc7d4d08b477e80211b3fe5b267ba341a84f78b8be"},
+    {file = "pysam-0.19.0-cp39-cp39-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:2911e3760dd2b709c686f075146787b8bda35629093352c28a7e52ac00ddaffc"},
+    {file = "pysam-0.19.0.tar.gz", hash = "sha256:dcc052566f9509fd93b2a2664f094a13f016fd60cdd189e05fb4eafa0c89505b"},
 ]
 pytest = [
     {file = "pytest-7.2.0-py3-none-any.whl", hash = "sha256:892f933d339f068883b6fd5a459f03d85bfcb355e4981e146d2c7616c21fef71"},

From a5a5cea9a4d2ea621be6aa4c6200665bcb493034 Mon Sep 17 00:00:00 2001
From: Arya Massarat <23412689+aryarm@users.noreply.github.com>
Date: Sat, 5 Nov 2022 23:36:55 -0700
Subject: [PATCH 03/10] add nox and friends to the project

---
 .gitignore     |   3 +-
 noxfile.py     |  60 +++++++++++
 poetry.lock    | 283 +++++++++++++++++++++++++++++++++++++++++++------
 pyproject.toml |  10 +-
 4 files changed, 320 insertions(+), 36 deletions(-)
 create mode 100644 noxfile.py

diff --git a/.gitignore b/.gitignore
index f282a23d..b9a163cd 100644
--- a/.gitignore
+++ b/.gitignore
@@ -8,6 +8,7 @@ docs/_build/
 __pycache__
 # pytest cache
 .pytest_cache
+.coverage
 # poetry
 dist/
 
@@ -18,4 +19,4 @@ dist/
 test.par
 test.phen
 example_simgenotype.bp
-example_simgenotype.vcf
\ No newline at end of file
+example_simgenotype.vcf
diff --git a/noxfile.py b/noxfile.py
new file mode 100644
index 00000000..fc7b5bb8
--- /dev/null
+++ b/noxfile.py
@@ -0,0 +1,60 @@
+"""Nox sessions."""
+import os
+import sys
+import shutil
+from pathlib import Path
+
+import nox
+from nox_poetry import Session
+from nox_poetry import session
+
+
+package = "haptools"
+python_versions = ["3.10", "3.9", "3.8", "3.7"]
+nox.needs_version = ">= 2021.6.6"
+nox.options.sessions = (
+    "tests",
+    "docs",
+)
+
+
+@session(python=python_versions)
+def tests(session: Session) -> None:
+    """Run the test suite."""
+    session.install(".[tests]")
+    session.install("coverage[toml]")
+
+    try:
+        session.run("coverage", "run", "--parallel", "-m", "pytest", *session.posargs)
+    finally:
+        if session.interactive:
+            session.notify("coverage", posargs=[])
+
+
+@session(python=python_versions[-1])
+def coverage(session: Session) -> None:
+    """Produce the coverage report."""
+    args = session.posargs or ["report"]
+
+    session.install("coverage[toml]")
+
+    if not session.posargs and any(Path().glob(".coverage.*")):
+        session.run("coverage", "combine")
+
+    session.run("coverage", *args)
+
+
+@session(name="docs", python=python_versions[-1])
+def docs(session: Session) -> None:
+    """Build the documentation."""
+    args = session.posargs or ["docs", "docs/_build"]
+    if not session.posargs and "FORCE_COLOR" in os.environ:
+        args.insert(0, "--color")
+
+    session.install(".[docs]")
+
+    build_dir = Path("docs", "_build")
+    if build_dir.exists():
+        shutil.rmtree(build_dir)
+
+    session.run("sphinx-build", *args)
diff --git a/poetry.lock b/poetry.lock
index 579d1045..a996ac13 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -14,6 +14,20 @@ category = "dev"
 optional = false
 python-versions = "*"
 
+[[package]]
+name = "argcomplete"
+version = "2.0.0"
+description = "Bash tab completion for argparse"
+category = "dev"
+optional = false
+python-versions = ">=3.6"
+
+[package.dependencies]
+importlib-metadata = {version = ">=0.23,<5", markers = "python_version == \"3.7\""}
+
+[package.extras]
+test = ["coverage", "flake8", "pexpect", "wheel"]
+
 [[package]]
 name = "attrs"
 version = "22.1.0"
@@ -23,10 +37,10 @@ optional = false
 python-versions = ">=3.5"
 
 [package.extras]
-dev = ["cloudpickle", "coverage[toml] (>=5.0.2)", "furo", "hypothesis", "mypy (>=0.900,!=0.940)", "pre-commit", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "sphinx", "sphinx-notfound-page", "zope.interface"]
-docs = ["furo", "sphinx", "sphinx-notfound-page", "zope.interface"]
-tests = ["cloudpickle", "coverage[toml] (>=5.0.2)", "hypothesis", "mypy (>=0.900,!=0.940)", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "zope.interface"]
-tests_no_zope = ["cloudpickle", "coverage[toml] (>=5.0.2)", "hypothesis", "mypy (>=0.900,!=0.940)", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins"]
+dev = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "mypy (>=0.900,!=0.940)", "pytest-mypy-plugins", "zope.interface", "furo", "sphinx", "sphinx-notfound-page", "pre-commit", "cloudpickle"]
+docs = ["furo", "sphinx", "zope.interface", "sphinx-notfound-page"]
+tests = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "mypy (>=0.900,!=0.940)", "pytest-mypy-plugins", "zope.interface", "cloudpickle"]
+tests_no_zope = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "mypy (>=0.900,!=0.940)", "pytest-mypy-plugins", "cloudpickle"]
 
 [[package]]
 name = "babel"
@@ -123,6 +137,34 @@ humanfriendly = ">=9.1"
 [package.extras]
 cron = ["capturer (>=2.4)"]
 
+[[package]]
+name = "colorlog"
+version = "6.7.0"
+description = "Add colours to the output of Python's logging module."
+category = "dev"
+optional = false
+python-versions = ">=3.6"
+
+[package.dependencies]
+colorama = {version = "*", markers = "sys_platform == \"win32\""}
+
+[package.extras]
+development = ["black", "flake8", "mypy", "pytest", "types-colorama"]
+
+[[package]]
+name = "coverage"
+version = "6.5.0"
+description = "Code coverage measurement for Python"
+category = "dev"
+optional = false
+python-versions = ">=3.7"
+
+[package.dependencies]
+tomli = {version = "*", optional = true, markers = "python_full_version <= \"3.11.0a6\" and extra == \"toml\""}
+
+[package.extras]
+toml = ["tomli"]
+
 [[package]]
 name = "cycler"
 version = "0.11.0"
@@ -152,6 +194,14 @@ category = "dev"
 optional = false
 python-versions = ">=3.5"
 
+[[package]]
+name = "distlib"
+version = "0.3.6"
+description = "Distribution utilities"
+category = "dev"
+optional = false
+python-versions = "*"
+
 [[package]]
 name = "docutils"
 version = "0.17.1"
@@ -171,6 +221,18 @@ python-versions = ">=3.7"
 [package.extras]
 test = ["pytest (>=6)"]
 
+[[package]]
+name = "filelock"
+version = "3.8.0"
+description = "A platform independent file lock."
+category = "dev"
+optional = false
+python-versions = ">=3.7"
+
+[package.extras]
+docs = ["furo (>=2022.6.21)", "sphinx (>=5.1.1)", "sphinx-autodoc-typehints (>=1.19.1)"]
+testing = ["covdefaults (>=2.2)", "coverage (>=6.4.2)", "pytest (>=7.1.2)", "pytest-cov (>=3)", "pytest-timeout (>=2.1)"]
+
 [[package]]
 name = "fonttools"
 version = "4.38.0"
@@ -180,9 +242,9 @@ optional = false
 python-versions = ">=3.7"
 
 [package.extras]
-all = ["brotli (>=1.0.1)", "brotlicffi (>=0.8.0)", "fs (>=2.2.0,<3)", "lxml (>=4.0,<5)", "lz4 (>=1.7.4.2)", "matplotlib", "munkres", "scipy", "skia-pathops (>=0.5.0)", "sympy", "uharfbuzz (>=0.23.0)", "unicodedata2 (>=14.0.0)", "xattr", "zopfli (>=0.1.4)"]
+all = ["fs (>=2.2.0,<3)", "lxml (>=4.0,<5)", "zopfli (>=0.1.4)", "lz4 (>=1.7.4.2)", "matplotlib", "sympy", "skia-pathops (>=0.5.0)", "uharfbuzz (>=0.23.0)", "brotlicffi (>=0.8.0)", "scipy", "brotli (>=1.0.1)", "munkres", "unicodedata2 (>=14.0.0)", "xattr"]
 graphite = ["lz4 (>=1.7.4.2)"]
-interpolatable = ["munkres", "scipy"]
+interpolatable = ["scipy", "munkres"]
 lxml = ["lxml (>=4.0,<5)"]
 pathops = ["skia-pathops (>=0.5.0)"]
 plot = ["matplotlib"]
@@ -191,7 +253,7 @@ symfont = ["sympy"]
 type1 = ["xattr"]
 ufo = ["fs (>=2.2.0,<3)"]
 unicode = ["unicodedata2 (>=14.0.0)"]
-woff = ["brotli (>=1.0.1)", "brotlicffi (>=0.8.0)", "zopfli (>=0.1.4)"]
+woff = ["zopfli (>=0.1.4)", "brotlicffi (>=0.8.0)", "brotli (>=1.0.1)"]
 
 [[package]]
 name = "humanfriendly"
@@ -234,9 +296,9 @@ typing-extensions = {version = ">=3.6.4", markers = "python_version < \"3.8\""}
 zipp = ">=0.5"
 
 [package.extras]
-docs = ["furo", "jaraco.packaging (>=9)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)"]
+docs = ["sphinx (>=3.5)", "jaraco.packaging (>=9)", "rst.linker (>=1.9)", "furo", "jaraco.tidelift (>=1.4)"]
 perf = ["ipython"]
-testing = ["flake8 (<5)", "flufl.flake8", "importlib-resources (>=1.3)", "packaging", "pyfakefs", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=1.3)", "pytest-flake8", "pytest-mypy (>=0.9.1)", "pytest-perf (>=0.9.2)"]
+testing = ["pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-flake8", "flake8 (<5)", "pytest-cov", "pytest-enabler (>=1.3)", "packaging", "pyfakefs", "flufl.flake8", "pytest-perf (>=0.9.2)", "pytest-black (>=0.3.7)", "pytest-mypy (>=0.9.1)", "importlib-resources (>=1.3)"]
 
 [[package]]
 name = "iniconfig"
@@ -273,10 +335,10 @@ doc = ["Sphinx (>=1.3)"]
 kernel = ["ipykernel"]
 nbconvert = ["nbconvert"]
 nbformat = ["nbformat"]
-notebook = ["ipywidgets", "notebook"]
+notebook = ["notebook", "ipywidgets"]
 parallel = ["ipyparallel"]
 qtconsole = ["qtconsole"]
-test = ["ipykernel", "nbformat", "nose (>=0.10.1)", "numpy (>=1.17)", "pygments", "requests", "testpath"]
+test = ["nose (>=0.10.1)", "requests", "testpath", "pygments", "nbformat", "ipykernel", "numpy (>=1.17)"]
 
 [[package]]
 name = "jedi"
@@ -364,6 +426,39 @@ category = "dev"
 optional = false
 python-versions = "*"
 
+[[package]]
+name = "nox"
+version = "2022.8.7"
+description = "Flexible test automation."
+category = "dev"
+optional = false
+python-versions = ">=3.7"
+
+[package.dependencies]
+argcomplete = ">=1.9.4,<3.0"
+colorlog = ">=2.6.1,<7.0.0"
+importlib-metadata = {version = "*", markers = "python_version < \"3.8\""}
+packaging = ">=20.9"
+py = ">=1.4,<2.0.0"
+typing-extensions = {version = ">=3.7.4", markers = "python_version < \"3.8\""}
+virtualenv = ">=14"
+
+[package.extras]
+tox_to_nox = ["jinja2", "tox"]
+
+[[package]]
+name = "nox-poetry"
+version = "1.0.1"
+description = "nox-poetry"
+category = "dev"
+optional = false
+python-versions = ">=3.7,<4.0"
+
+[package.dependencies]
+nox = ">=2020.8.22"
+packaging = ">=20.9"
+tomlkit = ">=0.7"
+
 [[package]]
 name = "numpy"
 version = "1.21.6"
@@ -385,7 +480,7 @@ Jinja2 = ">=2.10"
 sphinx = ">=4.2"
 
 [package.extras]
-testing = ["matplotlib", "pytest", "pytest-cov"]
+testing = ["pytest", "pytest-cov", "matplotlib"]
 
 [[package]]
 name = "packaging"
@@ -466,8 +561,8 @@ optional = false
 python-versions = ">=3.7"
 
 [package.extras]
-docs = ["furo (>=2021.7.5b38)", "proselint (>=0.10.2)", "sphinx (>=4)", "sphinx-autodoc-typehints (>=1.12)"]
-test = ["appdirs (==1.4.4)", "pytest (>=6)", "pytest-cov (>=2.7)", "pytest-mock (>=3.6)"]
+docs = ["furo (>=2021.7.5b38)", "proselint (>=0.10.2)", "sphinx-autodoc-typehints (>=1.12)", "sphinx (>=4)"]
+test = ["appdirs (==1.4.4)", "pytest-cov (>=2.7)", "pytest-mock (>=3.6)", "pytest (>=6)"]
 
 [[package]]
 name = "pluggy"
@@ -503,6 +598,14 @@ category = "dev"
 optional = false
 python-versions = "*"
 
+[[package]]
+name = "py"
+version = "1.11.0"
+description = "library with cross-python path, ini-parsing, io, code, log facilities"
+category = "dev"
+optional = false
+python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
+
 [[package]]
 name = "pygments"
 version = "2.13.0"
@@ -523,7 +626,7 @@ optional = false
 python-versions = ">=3.6.8"
 
 [package.extras]
-diagrams = ["jinja2", "railroad-diagrams"]
+diagrams = ["railroad-diagrams", "jinja2"]
 
 [[package]]
 name = "pyreadline"
@@ -668,8 +771,8 @@ sphinxcontrib-serializinghtml = ">=1.1.5"
 
 [package.extras]
 docs = ["sphinxcontrib-websupport"]
-lint = ["docutils-stubs", "flake8 (>=3.5.0)", "flake8-bugbear", "flake8-comprehensions", "flake8-simplify", "isort", "mypy (>=0.981)", "sphinx-lint", "types-requests", "types-typed-ast"]
-test = ["cython", "html5lib", "pytest (>=4.6)", "typed-ast"]
+lint = ["flake8 (>=3.5.0)", "flake8-comprehensions", "flake8-bugbear", "flake8-simplify", "isort", "mypy (>=0.981)", "sphinx-lint", "docutils-stubs", "types-typed-ast", "types-requests"]
+test = ["pytest (>=4.6)", "html5lib", "typed-ast", "cython"]
 
 [[package]]
 name = "sphinx-autodoc-typehints"
@@ -683,8 +786,8 @@ python-versions = ">=3.7"
 sphinx = ">=5.3"
 
 [package.extras]
-docs = ["furo (>=2022.9.29)", "sphinx (>=5.3)", "sphinx-autodoc-typehints (>=1.19.4)"]
-testing = ["covdefaults (>=2.2)", "coverage (>=6.5)", "diff-cover (>=7.0.1)", "nptyping (>=2.3.1)", "pytest (>=7.2)", "pytest-cov (>=4)", "sphobjinv (>=2.2.2)", "typing-extensions (>=4.4)"]
+docs = ["furo (>=2022.9.29)", "sphinx-autodoc-typehints (>=1.19.4)", "sphinx (>=5.3)"]
+testing = ["covdefaults (>=2.2)", "coverage (>=6.5)", "diff-cover (>=7.0.1)", "nptyping (>=2.3.1)", "pytest-cov (>=4)", "pytest (>=7.2)", "sphobjinv (>=2.2.2)", "typing-extensions (>=4.4)"]
 type-comment = ["typed-ast (>=1.5.4)"]
 
 [[package]]
@@ -713,7 +816,7 @@ docutils = "<0.18"
 sphinx = ">=1.6,<6"
 
 [package.extras]
-dev = ["bump2version", "sphinxcontrib-httpdomain", "transifex-client", "wheel"]
+dev = ["transifex-client", "sphinxcontrib-httpdomain", "bump2version", "wheel"]
 
 [[package]]
 name = "sphinxcontrib-applehelp"
@@ -724,7 +827,7 @@ optional = false
 python-versions = ">=3.5"
 
 [package.extras]
-lint = ["docutils-stubs", "flake8", "mypy"]
+lint = ["flake8", "mypy", "docutils-stubs"]
 test = ["pytest"]
 
 [[package]]
@@ -736,7 +839,7 @@ optional = false
 python-versions = ">=3.5"
 
 [package.extras]
-lint = ["docutils-stubs", "flake8", "mypy"]
+lint = ["flake8", "mypy", "docutils-stubs"]
 test = ["pytest"]
 
 [[package]]
@@ -748,8 +851,8 @@ optional = false
 python-versions = ">=3.6"
 
 [package.extras]
-lint = ["docutils-stubs", "flake8", "mypy"]
-test = ["html5lib", "pytest"]
+lint = ["flake8", "mypy", "docutils-stubs"]
+test = ["pytest", "html5lib"]
 
 [[package]]
 name = "sphinxcontrib-jsmath"
@@ -760,7 +863,7 @@ optional = false
 python-versions = ">=3.5"
 
 [package.extras]
-test = ["flake8", "mypy", "pytest"]
+test = ["pytest", "flake8", "mypy"]
 
 [[package]]
 name = "sphinxcontrib-qthelp"
@@ -771,7 +874,7 @@ optional = false
 python-versions = ">=3.5"
 
 [package.extras]
-lint = ["docutils-stubs", "flake8", "mypy"]
+lint = ["flake8", "mypy", "docutils-stubs"]
 test = ["pytest"]
 
 [[package]]
@@ -783,7 +886,7 @@ optional = false
 python-versions = ">=3.5"
 
 [package.extras]
-lint = ["docutils-stubs", "flake8", "mypy"]
+lint = ["flake8", "mypy", "docutils-stubs"]
 test = ["pytest"]
 
 [[package]]
@@ -794,6 +897,14 @@ category = "main"
 optional = false
 python-versions = ">=3.7"
 
+[[package]]
+name = "tomlkit"
+version = "0.11.6"
+description = "Style preserving TOML library"
+category = "dev"
+optional = false
+python-versions = ">=3.6"
+
 [[package]]
 name = "traitlets"
 version = "5.5.0"
@@ -831,10 +942,28 @@ optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*, <4"
 
 [package.extras]
-brotli = ["brotli (>=1.0.9)", "brotlicffi (>=0.8.0)", "brotlipy (>=0.6.0)"]
-secure = ["certifi", "cryptography (>=1.3.4)", "idna (>=2.0.0)", "ipaddress", "pyOpenSSL (>=0.14)", "urllib3-secure-extra"]
+brotli = ["brotlicffi (>=0.8.0)", "brotli (>=1.0.9)", "brotlipy (>=0.6.0)"]
+secure = ["pyOpenSSL (>=0.14)", "cryptography (>=1.3.4)", "idna (>=2.0.0)", "certifi", "urllib3-secure-extra", "ipaddress"]
 socks = ["PySocks (>=1.5.6,!=1.5.7,<2.0)"]
 
+[[package]]
+name = "virtualenv"
+version = "20.16.6"
+description = "Virtual Python Environment builder"
+category = "dev"
+optional = false
+python-versions = ">=3.6"
+
+[package.dependencies]
+distlib = ">=0.3.6,<1"
+filelock = ">=3.4.1,<4"
+importlib-metadata = {version = ">=4.8.3", markers = "python_version < \"3.8\""}
+platformdirs = ">=2.4,<3"
+
+[package.extras]
+docs = ["proselint (>=0.13)", "sphinx (>=5.3)", "sphinx-argparse (>=0.3.2)", "sphinx-rtd-theme (>=1)", "towncrier (>=22.8)"]
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     {file = "Pygments-2.13.0-py3-none-any.whl", hash = "sha256:f643f331ab57ba3c9d89212ee4a2dabc6e94f117cf4eefde99a0574720d14c42"},
     {file = "Pygments-2.13.0.tar.gz", hash = "sha256:56a8508ae95f98e2b9bdf93a6be5ae3f7d8af858b43e02c5a2ff083726be40c1"},
@@ -1406,6 +1615,10 @@ tomli = [
     {file = "tomli-2.0.1-py3-none-any.whl", hash = "sha256:939de3e7a6161af0c887ef91b7d41a53e7c5a1ca976325f429cb46ea9bc30ecc"},
     {file = "tomli-2.0.1.tar.gz", hash = "sha256:de526c12914f0c550d15924c62d72abc48d6fe7364aa87328337a31007fe8a4f"},
 ]
+tomlkit = [
+    {file = "tomlkit-0.11.6-py3-none-any.whl", hash = "sha256:07de26b0d8cfc18f871aec595fda24d95b08fef89d147caa861939f37230bf4b"},
+    {file = "tomlkit-0.11.6.tar.gz", hash = "sha256:71b952e5721688937fb02cf9d354dbcf0785066149d2855e44531ebdd2b65d73"},
+]
 traitlets = [
     {file = "traitlets-5.5.0-py3-none-any.whl", hash = "sha256:1201b2c9f76097195989cdf7f65db9897593b0dfd69e4ac96016661bb6f0d30f"},
     {file = "traitlets-5.5.0.tar.gz", hash = "sha256:b122f9ff2f2f6c1709dab289a05555be011c87828e911c0cf4074b85cb780a79"},
@@ -1444,6 +1657,10 @@ urllib3 = [
     {file = "urllib3-1.26.12-py2.py3-none-any.whl", hash = "sha256:b930dd878d5a8afb066a637fbb35144fe7901e3b209d1cd4f524bd0e9deee997"},
     {file = "urllib3-1.26.12.tar.gz", hash = "sha256:3fa96cf423e6987997fc326ae8df396db2a8b7c667747d47ddd8ecba91f4a74e"},
 ]
+virtualenv = [
+    {file = "virtualenv-20.16.6-py3-none-any.whl", hash = "sha256:186ca84254abcbde98180fd17092f9628c5fe742273c02724972a1d8a2035108"},
+    {file = "virtualenv-20.16.6.tar.gz", hash = "sha256:530b850b523c6449406dfba859d6345e48ef19b8439606c5d74d7d3c9e14d76e"},
+]
 wcwidth = [
     {file = "wcwidth-0.2.5-py2.py3-none-any.whl", hash = "sha256:beb4802a9cebb9144e99086eff703a642a13d6a0052920003a230f3294bbe784"},
     {file = "wcwidth-0.2.5.tar.gz", hash = "sha256:c4d647b99872929fdb7bdcaa4fbe7f01413ed3d98077df798530e5b04f116c83"},
diff --git a/pyproject.toml b/pyproject.toml
index 753dd386..2752288d 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -40,6 +40,9 @@ sphinx-click = { version = ">=3.0.2" }
 pytest = ">=6.2.5"
 black = ">=22.3.0"
 ipython = ">=7.30.1"
+nox = ">=2022.8.7"
+nox-poetry = ">=1.0.1"
+coverage = {extras = ["toml"], version = ">=6.5.0"}
 
 [tool.poetry.extras]
 docs = [
@@ -50,8 +53,11 @@ docs = [
     "sphinx-click"
 ]
 
-test = [
-    "pytest"
+tests = [
+    "pytest",
+    "coverage",
+    "nox",
+    "nox-poetry"
 ]
 
 files = [

From b2a5cb21fae291a6f20d7d50be9b721ed5da723a Mon Sep 17 00:00:00 2001
From: Arya Massarat <23412689+aryarm@users.noreply.github.com>
Date: Sun, 6 Nov 2022 21:04:53 -0800
Subject: [PATCH 04/10] run test session with different conda environments

---
 .gitignore |  3 ++-
 noxfile.py | 21 ++++++++++++---------
 2 files changed, 14 insertions(+), 10 deletions(-)

diff --git a/.gitignore b/.gitignore
index b9a163cd..4a5c14dd 100644
--- a/.gitignore
+++ b/.gitignore
@@ -6,9 +6,10 @@ snakemake/out
 docs/_build/
 # python cache
 __pycache__
-# pytest cache
+# pytest and testing-related caches
 .pytest_cache
 .coverage
+.nox
 # poetry
 dist/
 
diff --git a/noxfile.py b/noxfile.py
index fc7b5bb8..7ac9db91 100644
--- a/noxfile.py
+++ b/noxfile.py
@@ -18,11 +18,18 @@
 )
 
 
-@session(python=python_versions)
+# detect whether mamba is installed
+conda_cmd = "conda"
+if (Path(os.getenv("CONDA_EXE")).parent / "mamba").exists():
+    conda_cmd = "mamba"
+conda_args = ["-c", "conda-forge"]
+
+
+@session(venv_backend=conda_cmd, venv_params=conda_args, python=python_versions)
 def tests(session: Session) -> None:
     """Run the test suite."""
-    session.install(".[tests]")
-    session.install("coverage[toml]")
+    session.conda_install("coverage[toml]", "pytest", channel="conda-forge")
+    session.install(".[files]")
 
     try:
         session.run("coverage", "run", "--parallel", "-m", "pytest", *session.posargs)
@@ -31,28 +38,24 @@ def tests(session: Session) -> None:
             session.notify("coverage", posargs=[])
 
 
-@session(python=python_versions[-1])
+@session(python=False)
 def coverage(session: Session) -> None:
     """Produce the coverage report."""
     args = session.posargs or ["report"]
 
-    session.install("coverage[toml]")
-
     if not session.posargs and any(Path().glob(".coverage.*")):
         session.run("coverage", "combine")
 
     session.run("coverage", *args)
 
 
-@session(name="docs", python=python_versions[-1])
+@session(python=False)
 def docs(session: Session) -> None:
     """Build the documentation."""
     args = session.posargs or ["docs", "docs/_build"]
     if not session.posargs and "FORCE_COLOR" in os.environ:
         args.insert(0, "--color")
 
-    session.install(".[docs]")
-
     build_dir = Path("docs", "_build")
     if build_dir.exists():
         shutil.rmtree(build_dir)

From e31fc82c04903157e4cc4a964f4f226b609a6122 Mon Sep 17 00:00:00 2001
From: Arya Massarat <23412689+aryarm@users.noreply.github.com>
Date: Sun, 6 Nov 2022 21:29:36 -0800
Subject: [PATCH 05/10] refmt docs/conf.py with black

---
 docs/conf.py | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/docs/conf.py b/docs/conf.py
index e0fe0d89..8932efaf 100644
--- a/docs/conf.py
+++ b/docs/conf.py
@@ -61,9 +61,9 @@
 html_static_path = []
 
 html_context = {
-    "display_github": True, # Integrate GitHub
-    "github_user": "CAST-genomics", # Username
-    "github_repo": "haptools", # Repo name
-    "github_version": "main", # Version
-    "conf_py_path": "/docs/", # Path in the checkout to the docs root
+    "display_github": True,  # Integrate GitHub
+    "github_user": "CAST-genomics",  # Username
+    "github_repo": "haptools",  # Repo name
+    "github_version": "main",  # Version
+    "conf_py_path": "/docs/",  # Path in the checkout to the docs root
 }

From d196a416cd722fd176037bf50eaf1cd9607e8602 Mon Sep 17 00:00:00 2001
From: Arya Massarat <23412689+aryarm@users.noreply.github.com>
Date: Sun, 6 Nov 2022 21:31:34 -0800
Subject: [PATCH 06/10] make hook_compressed compatible across py3.7-py3.10

---
 haptools/data/breakpoints.py |  5 ++---
 haptools/data/covariates.py  |  6 ------
 haptools/data/data.py        | 32 +++++++++++++++++++++++++++++++-
 haptools/data/genotypes.py   |  7 +++----
 haptools/data/haplotypes.py  |  6 +++---
 haptools/data/phenotypes.py  |  5 ++---
 haptools/index.py            |  3 +--
 haptools/ld.py               |  3 +--
 tests/test_index.py          | 22 +++++++++++++---------
 9 files changed, 56 insertions(+), 33 deletions(-)

diff --git a/haptools/data/breakpoints.py b/haptools/data/breakpoints.py
index 9b56e1ee..08b118d9 100644
--- a/haptools/data/breakpoints.py
+++ b/haptools/data/breakpoints.py
@@ -5,7 +5,6 @@
 from collections import namedtuple
 from collections.abc import Iterable
 from logging import getLogger, Logger
-from fileinput import hook_compressed
 
 import numpy as np
 import numpy.typing as npt
@@ -118,7 +117,7 @@ def __iter__(self, samples: set[str] = None) -> Iterable[str, SampleBlocks]:
             first as a string, and then followed by its SampleBlocks
         """
         # TODO: add a region parameter
-        bps = hook_compressed(self.fname, mode="rt")
+        bps = self.hook_compressed(self.fname, mode="r")
         bp_text = csv.reader(bps, delimiter="\t")
         samp = None
         blocks = {}
@@ -346,7 +345,7 @@ def write(self):
         >>> }
         >>> breakpoints.write()
         """
-        with hook_compressed(self.fname, mode="wt") as bkpts:
+        with self.hook_compressed(self.fname, mode="w") as bkpts:
             csv_writer = csv.writer(
                 bkpts, delimiter="\t", dialect="unix", quoting=csv.QUOTE_NONE
             )
diff --git a/haptools/data/covariates.py b/haptools/data/covariates.py
index 97cfb52c..47de25e4 100644
--- a/haptools/data/covariates.py
+++ b/haptools/data/covariates.py
@@ -1,13 +1,7 @@
 from __future__ import annotations
-from csv import reader
 from pathlib import Path
-from collections import namedtuple
 from logging import getLogger, Logger
-from fileinput import hook_compressed
 
-import numpy as np
-
-from .data import Data
 from .phenotypes import Phenotypes
 
 
diff --git a/haptools/data/data.py b/haptools/data/data.py
index 23dbb63a..915dc604 100644
--- a/haptools/data/data.py
+++ b/haptools/data/data.py
@@ -1,7 +1,9 @@
 from __future__ import annotations
+import os
+import gzip
 from csv import reader
 from pathlib import Path
-from typing import Iterator
+from typing import Iterator, IO
 from collections import namedtuple
 from abc import ABC, abstractmethod
 from logging import getLogger, Logger
@@ -78,3 +80,31 @@ def __iter__(self) -> Iterator[namedtuple]:
             namedtuple containing each of the class properties
         """
         pass
+
+    @staticmethod
+    def hook_compressed(filename: str, mode: str) -> IO:
+        """
+        A utility to help open files regardless of their compression
+
+        Based off of python's fileinput.hook_compressed and copied from
+        https://stackoverflow.com/a/64106815/16815703
+
+        Parameters
+        ----------
+        filename : str
+            The path to the file
+        mode : str
+            Either 'r' for read or 'w' for write
+
+        Returns
+        -------
+        IO
+            The resolved file object
+        """
+        if "b" not in mode:
+            mode += "t"
+        ext = os.path.splitext(filename)[1]
+        if ext == ".gz":
+            return gzip.open(filename, mode)
+        else:
+            return open(filename, mode)
diff --git a/haptools/data/genotypes.py b/haptools/data/genotypes.py
index 14e75018..14dac352 100644
--- a/haptools/data/genotypes.py
+++ b/haptools/data/genotypes.py
@@ -4,7 +4,6 @@
 from pathlib import Path
 from typing import Iterator
 from logging import getLogger, Logger
-from fileinput import hook_compressed
 from collections import namedtuple, Counter
 
 import numpy as np
@@ -737,7 +736,7 @@ def read_samples(self, samples: list[str] = None):
             self.log.warning("Sample data has already been loaded. Overriding.")
         if samples is not None and not isinstance(samples, set):
             samples = set(samples)
-        with hook_compressed(self.fname.with_suffix(".psam"), mode="rt") as psam:
+        with self.hook_compressed(self.fname.with_suffix(".psam"), mode="r") as psam:
             psamples = reader(psam, delimiter="\t")
             # find the line that declares the header
             for header in psamples:
@@ -862,7 +861,7 @@ def _iterate_variants(
             region = re.split(":|-", region)
             if len(region) > 1:
                 region[1:] = [int(pos) for pos in region[1:] if pos]
-        with hook_compressed(self.fname.with_suffix(".pvar"), mode="rt") as pvar:
+        with self.hook_compressed(self.fname.with_suffix(".pvar"), mode="r") as pvar:
             pvariants = reader(pvar, delimiter="\t")
             # find the line that declares the header
             for header in pvariants:
@@ -1158,7 +1157,7 @@ def write_samples(self):
 
         This method is called automatically by :py:meth:`~.GenotypesPLINK.write`
         """
-        with hook_compressed(self.fname.with_suffix(".psam"), mode="wt") as psam:
+        with self.hook_compressed(self.fname.with_suffix(".psam"), mode="w") as psam:
             psam.write("#IID\n")
             psam.write("\n".join(self.samples))
             psam.write("\n")
diff --git a/haptools/data/haplotypes.py b/haptools/data/haplotypes.py
index aa7bf41e..0accf367 100644
--- a/haptools/data/haplotypes.py
+++ b/haptools/data/haplotypes.py
@@ -1,8 +1,8 @@
 from __future__ import annotations
+import os
 from pathlib import Path
 from functools import total_ordering
 from logging import getLogger, Logger
-from fileinput import hook_compressed
 from dataclasses import dataclass, field, fields
 from typing import Iterator, get_type_hints, Generator, Callable
 
@@ -959,7 +959,7 @@ def __iter__(
         else:
             # the file is not indexed, so we can't assume it's sorted, either
             # use hook_compressed to automatically handle gz files
-            with hook_compressed(self.fname, mode="rt") as haps:
+            with self.hook_compressed(self.fname, mode="r") as haps:
                 self.log.info("Not taking advantage of indexing.")
                 header_lines = []
                 for line in haps:
@@ -1047,7 +1047,7 @@ def write(self):
         >>> haplotypes.data = {'H1': Haplotype('chr1', 0, 10, 'H1')}
         >>> haplotypes.write()
         """
-        with hook_compressed(self.fname, mode="wt") as haps:
+        with self.hook_compressed(self.fname, mode="w") as haps:
             for line in self.to_str():
                 haps.write(line + "\n")
 
diff --git a/haptools/data/phenotypes.py b/haptools/data/phenotypes.py
index d534cc76..b13ba7d2 100644
--- a/haptools/data/phenotypes.py
+++ b/haptools/data/phenotypes.py
@@ -4,7 +4,6 @@
 from io import TextIOBase
 from collections.abc import Iterable
 from logging import getLogger, Logger
-from fileinput import hook_compressed
 from collections import namedtuple, Counter
 
 import numpy as np
@@ -145,7 +144,7 @@ def __iter__(self, samples: list[str] = None) -> Iterable[namedtuple]:
         Iterable[namedtuple]
             See documentation for :py:meth:`~.Phenotypes._iterate`
         """
-        phens = hook_compressed(self.fname, mode="rt")
+        phens = self.hook_compressed(self.fname, mode="r")
         phen_text = reader(phens, delimiter="\t")
         # ignore all of the comment lines
         while True:
@@ -192,7 +191,7 @@ def write(self):
             names[idx] = name + suffix
             uniq_names[name] += 1
         # now we can finally write the file
-        with hook_compressed(self.fname, mode="wt") as phens:
+        with self.hook_compressed(self.fname, mode="w") as phens:
             phens.write("#IID\t" + "\t".join(names) + "\n")
             formatter = {"float_kind": lambda x: "%.2f" % x}
             for samp, phen in zip(self.samples, self.data):
diff --git a/haptools/index.py b/haptools/index.py
index 5b2eaed7..0cf8a1a3 100644
--- a/haptools/index.py
+++ b/haptools/index.py
@@ -3,7 +3,6 @@
 import logging
 import tempfile
 from pathlib import Path
-from fileinput import hook_compressed
 
 from pysam import tabix_index
 
@@ -70,7 +69,7 @@ def index_haps(
         # copy the file to a tmp location in case the input is /dev/stdin
         # or a file that might otherwise be deleted by tabix_index afterward
         with tempfile.NamedTemporaryFile(delete=False, mode="wt") as tmp:
-            with hook_compressed(str(hp.fname), mode="rt") as haps:
+            with data.Data.hook_compressed(str(hp.fname), mode="r") as haps:
                 hp.fname = Path(tmp.name)
                 tmp.write(haps.read())
 
diff --git a/haptools/ld.py b/haptools/ld.py
index 27ae2474..75cffc33 100644
--- a/haptools/ld.py
+++ b/haptools/ld.py
@@ -1,7 +1,6 @@
 from __future__ import annotations
 import logging
 from pathlib import Path
-from fileinput import hook_compressed
 from dataclasses import dataclass, field
 
 import numpy as np
@@ -198,7 +197,7 @@ def calc_ld(
 
     if from_gts:
         log.info("Computing LD between genotypes and the target")
-        with hook_compressed(output, mode="wt") as ld_file:
+        with data.Data.hook_compressed(output, mode="w") as ld_file:
             log.info("Outputting .ld file with LD values")
             ld_file.write("CHR\tBP\tSNP\tR\n")
             for idx, variant in enumerate(gt.variants[["chrom", "pos", "id"]]):
diff --git a/tests/test_index.py b/tests/test_index.py
index 58185eec..04ca4c68 100644
--- a/tests/test_index.py
+++ b/tests/test_index.py
@@ -1,10 +1,10 @@
 import shutil
 from pathlib import Path
-from fileinput import hook_compressed
 
 import numpy as np
 from click.testing import CliRunner
 
+from haptools.data import Data
 from haptools.__main__ import main
 
 DATADIR = Path(__file__).parent.joinpath("data")
@@ -23,15 +23,17 @@ def test_basic(capfd):
     captured = capfd.readouterr()
     assert captured.out == ""
     # check that the output .hap.gz file is the same as the file in tests/data/
-    with hook_compressed(tmp_file.with_suffix(".hap.gz"), mode="rt") as haps:
+    with Data.hook_compressed(tmp_file.with_suffix(".hap.gz"), mode="rt") as haps:
         haps = filter(lambda l: not l.startswith("#"), haps.read().splitlines())
-        with hook_compressed(file.with_suffix(".hap.gz"), mode="rt") as expected:
+        with Data.hook_compressed(file.with_suffix(".hap.gz"), mode="rt") as expected:
             exp = filter(lambda l: not l.startswith("#"), expected.read().splitlines())
             assert list(haps) == list(exp)
     # check that the output .hap.gz.tbi file is the same, too
     tbi_nocomment = ".nocomment.hap.gz.tbi"
-    with hook_compressed(tmp_file.with_suffix(".hap.gz.tbi"), mode="rb") as haps:
-        with hook_compressed(file.with_suffix(tbi_nocomment), mode="rb") as expected:
+    with Data.hook_compressed(tmp_file.with_suffix(".hap.gz.tbi"), mode="rb") as haps:
+        with Data.hook_compressed(
+            file.with_suffix(tbi_nocomment), mode="rb"
+        ) as expected:
             assert haps.read() == expected.read()
     assert result.exit_code == 0
 
@@ -47,13 +49,15 @@ def test_no_sort(capfd):
     captured = capfd.readouterr()
     assert captured.out == ""
     # check that the output .hap.gz file is the same as the file in tests/data/
-    with hook_compressed("test.hap.gz", mode="rt") as haps:
-        with hook_compressed("tests/data/basic.hap.gz", mode="rt") as expected:
+    with Data.hook_compressed("test.hap.gz", mode="rt") as haps:
+        with Data.hook_compressed("tests/data/basic.hap.gz", mode="rt") as expected:
             assert haps.read() == expected.read()
     # check that the output .hap.gz.tbi file is the same, too
     tbi_nocomment = ".comment.hap.gz.tbi"
-    with hook_compressed("test.hap.gz.tbi", mode="rb") as haps:
-        with hook_compressed("tests/data/basic" + tbi_nocomment, mode="rb") as expected:
+    with Data.hook_compressed("test.hap.gz.tbi", mode="rb") as haps:
+        with Data.hook_compressed(
+            "tests/data/basic" + tbi_nocomment, mode="rb"
+        ) as expected:
             assert haps.read() == expected.read()
     assert result.exit_code == 0
 

From bcc775dcc11d50e22df3fc425e4cb8dedf356fa3 Mon Sep 17 00:00:00 2001
From: Arya Massarat <23412689+aryarm@users.noreply.github.com>
Date: Sun, 6 Nov 2022 22:55:34 -0800
Subject: [PATCH 07/10] add linting to our noxfile

---
 docs/project_info/contributing.rst | 16 ++++++----
 noxfile.py                         | 47 ++++++++++++++++++------------
 2 files changed, 40 insertions(+), 23 deletions(-)

diff --git a/docs/project_info/contributing.rst b/docs/project_info/contributing.rst
index 2f30db4e..228cff24 100644
--- a/docs/project_info/contributing.rst
+++ b/docs/project_info/contributing.rst
@@ -96,26 +96,32 @@ For example, to add a pypi dependency to our list and install it, just run
 -----------
 Code Checks
 -----------
-Before creating your pull request, please do the following.
+Before creating your pull request, please run our code checks through ``nox``.
+
+.. code-block:: bash
+
+    nox
+
+You can also execute each of our code checks individually.
 
 1. Format the code correctly
 
     .. code-block:: bash
 
-        black .
+        nox --session=lint
 
 2. If you made changes to the docs, check that they appear correctly.
 
     .. code-block:: bash
 
-        ( cd docs && sphinx-build -M html . _build )
-        open docs/_build/html/index.html
+        nox --session=docs
+        open docs/_build/index.html
 
 3. Run all of the tests
 
     .. code-block:: bash
 
-        pytest tests/
+        nox --session=tests
 
 -----
 Style
diff --git a/noxfile.py b/noxfile.py
index 7ac9db91..29ee521e 100644
--- a/noxfile.py
+++ b/noxfile.py
@@ -10,11 +10,12 @@
 
 
 package = "haptools"
-python_versions = ["3.10", "3.9", "3.8", "3.7"]
+python_versions = ["3.7", "3.8", "3.9", "3.10"]
 nox.needs_version = ">= 2021.6.6"
 nox.options.sessions = (
-    "tests",
     "docs",
+    "lint",
+    "tests",
 )
 
 
@@ -25,11 +26,35 @@
 conda_args = ["-c", "conda-forge"]
 
 
+@session(python=False)
+def docs(session: Session) -> None:
+    """Build the documentation."""
+    args = session.posargs or ["docs", "docs/_build"]
+    if not session.posargs and "FORCE_COLOR" in os.environ:
+        args.insert(0, "--color")
+
+    build_dir = Path("docs", "_build")
+    if build_dir.exists():
+        shutil.rmtree(build_dir)
+
+    session.run("sphinx-build", *args)
+
+
+@session(python=False)
+def lint(session: Session) -> None:
+    """Lint our code."""
+    session.run("black", "--check", ".")
+
+
 @session(venv_backend=conda_cmd, venv_params=conda_args, python=python_versions)
 def tests(session: Session) -> None:
     """Run the test suite."""
-    session.conda_install("coverage[toml]", "pytest", channel="conda-forge")
-    session.install(".[files]")
+    session.conda_install(
+        "coverage[toml]", "pytest", "numpy>=1.20.0", channel="conda-forge"
+    )
+    # TODO: change this to ".[files]" once plink-ng Alpha 3.8 is released
+    # https://github.com/chrchang/plink-ng/releases
+    session.install(".")
 
     try:
         session.run("coverage", "run", "--parallel", "-m", "pytest", *session.posargs)
@@ -47,17 +72,3 @@ def coverage(session: Session) -> None:
         session.run("coverage", "combine")
 
     session.run("coverage", *args)
-
-
-@session(python=False)
-def docs(session: Session) -> None:
-    """Build the documentation."""
-    args = session.posargs or ["docs", "docs/_build"]
-    if not session.posargs and "FORCE_COLOR" in os.environ:
-        args.insert(0, "--color")
-
-    build_dir = Path("docs", "_build")
-    if build_dir.exists():
-        shutil.rmtree(build_dir)
-
-    session.run("sphinx-build", *args)

From da3c5ad90253259afec12a03162860b343a7f758 Mon Sep 17 00:00:00 2001
From: Arya Massarat <23412689+aryarm@users.noreply.github.com>
Date: Mon, 7 Nov 2022 08:52:47 -0800
Subject: [PATCH 08/10] update haptools to v0.0.3

---
 poetry.lock    | 2 +-
 pyproject.toml | 4 ++--
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index a996ac13..cad43e7f 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -992,7 +992,7 @@ tests = []
 [metadata]
 lock-version = "1.1"
 python-versions = ">=3.7,<3.11"
-content-hash = "4170889474821c2d0996119776b754e86fa0e805458ea37432502f88b3108318"
+content-hash = "c5917874417ca6c83911a0137187cce70403ea8b0e1840775d8de72ba6bcd530"
 
 [metadata.files]
 alabaster = [
diff --git a/pyproject.toml b/pyproject.toml
index 2752288d..d585e078 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "haptools"
-version = "0.0.2"
+version = "0.0.3"
 description = "Ancestry and haplotype aware simulation of genotypes and phenotypes for complex trait analysis"
 authors = ["Arya Massarat", "Michael Lamkin"]
 license = "MIT"
@@ -14,7 +14,7 @@ click = ">=8.0.3"
 pysam = ">=0.19.0"
 cyvcf2 = ">=0.30.14"
 matplotlib = ">=3.5.1"
-importlib-metadata = { version = ">=1.5.0,<5.0.0", python = "<3.8" }
+importlib-metadata = { version = ">=1.5.0", python = "<3.8" }
 Pgenlib = { version = ">=0.81.2", optional = true }
 
 # docs

From 52dbed5309856d1ed6a9fdc5ceb6651f8da5ed49 Mon Sep 17 00:00:00 2001
From: Arya Massarat <23412689+aryarm@users.noreply.github.com>
Date: Mon, 7 Nov 2022 09:34:07 -0800
Subject: [PATCH 09/10] remove importlib dependency since click depends on it,
 anyway

---
 poetry.lock    | 2 +-
 pyproject.toml | 1 -
 2 files changed, 1 insertion(+), 2 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index cad43e7f..f8432800 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -992,7 +992,7 @@ tests = []
 [metadata]
 lock-version = "1.1"
 python-versions = ">=3.7,<3.11"
-content-hash = "c5917874417ca6c83911a0137187cce70403ea8b0e1840775d8de72ba6bcd530"
+content-hash = "f7388f62aad37fb7bc483fa717525c73343b75e2ae9d084f6f772b0eb29f8fd6"
 
 [metadata.files]
 alabaster = [
diff --git a/pyproject.toml b/pyproject.toml
index d585e078..b87a736d 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -14,7 +14,6 @@ click = ">=8.0.3"
 pysam = ">=0.19.0"
 cyvcf2 = ">=0.30.14"
 matplotlib = ">=3.5.1"
-importlib-metadata = { version = ">=1.5.0", python = "<3.8" }
 Pgenlib = { version = ">=0.81.2", optional = true }
 
 # docs

From fd6cbe6df65f4689c2e1cede8f092871805ae37d Mon Sep 17 00:00:00 2001
From: Arya Massarat <23412689+aryarm@users.noreply.github.com>
Date: Mon, 7 Nov 2022 10:21:09 -0800
Subject: [PATCH 10/10] sync lock file with new poetry deps

---
 poetry.lock | 70 ++++++++++++++++++++++++++---------------------------
 1 file changed, 35 insertions(+), 35 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index f8432800..37a23f7f 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -37,10 +37,10 @@ optional = false
 python-versions = ">=3.5"
 
 [package.extras]
-dev = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "mypy (>=0.900,!=0.940)", "pytest-mypy-plugins", "zope.interface", "furo", "sphinx", "sphinx-notfound-page", "pre-commit", "cloudpickle"]
-docs = ["furo", "sphinx", "zope.interface", "sphinx-notfound-page"]
-tests = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "mypy (>=0.900,!=0.940)", "pytest-mypy-plugins", "zope.interface", "cloudpickle"]
-tests_no_zope = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "mypy (>=0.900,!=0.940)", "pytest-mypy-plugins", "cloudpickle"]
+dev = ["cloudpickle", "coverage[toml] (>=5.0.2)", "furo", "hypothesis", "mypy (>=0.900,!=0.940)", "pre-commit", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "sphinx", "sphinx-notfound-page", "zope.interface"]
+docs = ["furo", "sphinx", "sphinx-notfound-page", "zope.interface"]
+tests = ["cloudpickle", "coverage[toml] (>=5.0.2)", "hypothesis", "mypy (>=0.900,!=0.940)", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "zope.interface"]
+tests_no_zope = ["cloudpickle", "coverage[toml] (>=5.0.2)", "hypothesis", "mypy (>=0.900,!=0.940)", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins"]
 
 [[package]]
 name = "babel"
@@ -242,9 +242,9 @@ optional = false
 python-versions = ">=3.7"
 
 [package.extras]
-all = ["fs (>=2.2.0,<3)", "lxml (>=4.0,<5)", "zopfli (>=0.1.4)", "lz4 (>=1.7.4.2)", "matplotlib", "sympy", "skia-pathops (>=0.5.0)", "uharfbuzz (>=0.23.0)", "brotlicffi (>=0.8.0)", "scipy", "brotli (>=1.0.1)", "munkres", "unicodedata2 (>=14.0.0)", "xattr"]
+all = ["brotli (>=1.0.1)", "brotlicffi (>=0.8.0)", "fs (>=2.2.0,<3)", "lxml (>=4.0,<5)", "lz4 (>=1.7.4.2)", "matplotlib", "munkres", "scipy", "skia-pathops (>=0.5.0)", "sympy", "uharfbuzz (>=0.23.0)", "unicodedata2 (>=14.0.0)", "xattr", "zopfli (>=0.1.4)"]
 graphite = ["lz4 (>=1.7.4.2)"]
-interpolatable = ["scipy", "munkres"]
+interpolatable = ["munkres", "scipy"]
 lxml = ["lxml (>=4.0,<5)"]
 pathops = ["skia-pathops (>=0.5.0)"]
 plot = ["matplotlib"]
@@ -253,7 +253,7 @@ symfont = ["sympy"]
 type1 = ["xattr"]
 ufo = ["fs (>=2.2.0,<3)"]
 unicode = ["unicodedata2 (>=14.0.0)"]
-woff = ["zopfli (>=0.1.4)", "brotlicffi (>=0.8.0)", "brotli (>=1.0.1)"]
+woff = ["brotli (>=1.0.1)", "brotlicffi (>=0.8.0)", "zopfli (>=0.1.4)"]
 
 [[package]]
 name = "humanfriendly"
@@ -296,9 +296,9 @@ typing-extensions = {version = ">=3.6.4", markers = "python_version < \"3.8\""}
 zipp = ">=0.5"
 
 [package.extras]
-docs = ["sphinx (>=3.5)", "jaraco.packaging (>=9)", "rst.linker (>=1.9)", "furo", "jaraco.tidelift (>=1.4)"]
+docs = ["furo", "jaraco.packaging (>=9)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)"]
 perf = ["ipython"]
-testing = ["pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-flake8", "flake8 (<5)", "pytest-cov", "pytest-enabler (>=1.3)", "packaging", "pyfakefs", "flufl.flake8", "pytest-perf (>=0.9.2)", "pytest-black (>=0.3.7)", "pytest-mypy (>=0.9.1)", "importlib-resources (>=1.3)"]
+testing = ["flake8 (<5)", "flufl.flake8", "importlib-resources (>=1.3)", "packaging", "pyfakefs", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=1.3)", "pytest-flake8", "pytest-mypy (>=0.9.1)", "pytest-perf (>=0.9.2)"]
 
 [[package]]
 name = "iniconfig"
@@ -335,10 +335,10 @@ doc = ["Sphinx (>=1.3)"]
 kernel = ["ipykernel"]
 nbconvert = ["nbconvert"]
 nbformat = ["nbformat"]
-notebook = ["notebook", "ipywidgets"]
+notebook = ["ipywidgets", "notebook"]
 parallel = ["ipyparallel"]
 qtconsole = ["qtconsole"]
-test = ["nose (>=0.10.1)", "requests", "testpath", "pygments", "nbformat", "ipykernel", "numpy (>=1.17)"]
+test = ["ipykernel", "nbformat", "nose (>=0.10.1)", "numpy (>=1.17)", "pygments", "requests", "testpath"]
 
 [[package]]
 name = "jedi"
@@ -480,7 +480,7 @@ Jinja2 = ">=2.10"
 sphinx = ">=4.2"
 
 [package.extras]
-testing = ["pytest", "pytest-cov", "matplotlib"]
+testing = ["matplotlib", "pytest", "pytest-cov"]
 
 [[package]]
 name = "packaging"
@@ -554,15 +554,15 @@ tests = ["check-manifest", "coverage", "defusedxml", "markdown2", "olefile", "pa
 
 [[package]]
 name = "platformdirs"
-version = "2.5.2"
-description = "A small Python module for determining appropriate platform-specific dirs, e.g. a \"user data dir\"."
+version = "2.5.3"
+description = "A small Python package for determining appropriate platform-specific dirs, e.g. a \"user data dir\"."
 category = "dev"
 optional = false
 python-versions = ">=3.7"
 
 [package.extras]
-docs = ["furo (>=2021.7.5b38)", "proselint (>=0.10.2)", "sphinx-autodoc-typehints (>=1.12)", "sphinx (>=4)"]
-test = ["appdirs (==1.4.4)", "pytest-cov (>=2.7)", "pytest-mock (>=3.6)", "pytest (>=6)"]
+docs = ["furo (>=2022.9.29)", "proselint (>=0.13)", "sphinx (>=5.3)", "sphinx-autodoc-typehints (>=1.19.4)"]
+test = ["appdirs (==1.4.4)", "pytest (>=7.2)", "pytest-cov (>=4)", "pytest-mock (>=3.10)"]
 
 [[package]]
 name = "pluggy"
@@ -626,7 +626,7 @@ optional = false
 python-versions = ">=3.6.8"
 
 [package.extras]
-diagrams = ["railroad-diagrams", "jinja2"]
+diagrams = ["jinja2", "railroad-diagrams"]
 
 [[package]]
 name = "pyreadline"
@@ -771,8 +771,8 @@ sphinxcontrib-serializinghtml = ">=1.1.5"
 
 [package.extras]
 docs = ["sphinxcontrib-websupport"]
-lint = ["flake8 (>=3.5.0)", "flake8-comprehensions", "flake8-bugbear", "flake8-simplify", "isort", "mypy (>=0.981)", "sphinx-lint", "docutils-stubs", "types-typed-ast", "types-requests"]
-test = ["pytest (>=4.6)", "html5lib", "typed-ast", "cython"]
+lint = ["docutils-stubs", "flake8 (>=3.5.0)", "flake8-bugbear", "flake8-comprehensions", "flake8-simplify", "isort", "mypy (>=0.981)", "sphinx-lint", "types-requests", "types-typed-ast"]
+test = ["cython", "html5lib", "pytest (>=4.6)", "typed-ast"]
 
 [[package]]
 name = "sphinx-autodoc-typehints"
@@ -786,8 +786,8 @@ python-versions = ">=3.7"
 sphinx = ">=5.3"
 
 [package.extras]
-docs = ["furo (>=2022.9.29)", "sphinx-autodoc-typehints (>=1.19.4)", "sphinx (>=5.3)"]
-testing = ["covdefaults (>=2.2)", "coverage (>=6.5)", "diff-cover (>=7.0.1)", "nptyping (>=2.3.1)", "pytest-cov (>=4)", "pytest (>=7.2)", "sphobjinv (>=2.2.2)", "typing-extensions (>=4.4)"]
+docs = ["furo (>=2022.9.29)", "sphinx (>=5.3)", "sphinx-autodoc-typehints (>=1.19.4)"]
+testing = ["covdefaults (>=2.2)", "coverage (>=6.5)", "diff-cover (>=7.0.1)", "nptyping (>=2.3.1)", "pytest (>=7.2)", "pytest-cov (>=4)", "sphobjinv (>=2.2.2)", "typing-extensions (>=4.4)"]
 type-comment = ["typed-ast (>=1.5.4)"]
 
 [[package]]
@@ -816,7 +816,7 @@ docutils = "<0.18"
 sphinx = ">=1.6,<6"
 
 [package.extras]
-dev = ["transifex-client", "sphinxcontrib-httpdomain", "bump2version", "wheel"]
+dev = ["bump2version", "sphinxcontrib-httpdomain", "transifex-client", "wheel"]
 
 [[package]]
 name = "sphinxcontrib-applehelp"
@@ -827,7 +827,7 @@ optional = false
 python-versions = ">=3.5"
 
 [package.extras]
-lint = ["flake8", "mypy", "docutils-stubs"]
+lint = ["docutils-stubs", "flake8", "mypy"]
 test = ["pytest"]
 
 [[package]]
@@ -839,7 +839,7 @@ optional = false
 python-versions = ">=3.5"
 
 [package.extras]
-lint = ["flake8", "mypy", "docutils-stubs"]
+lint = ["docutils-stubs", "flake8", "mypy"]
 test = ["pytest"]
 
 [[package]]
@@ -851,8 +851,8 @@ optional = false
 python-versions = ">=3.6"
 
 [package.extras]
-lint = ["flake8", "mypy", "docutils-stubs"]
-test = ["pytest", "html5lib"]
+lint = ["docutils-stubs", "flake8", "mypy"]
+test = ["html5lib", "pytest"]
 
 [[package]]
 name = "sphinxcontrib-jsmath"
@@ -863,7 +863,7 @@ optional = false
 python-versions = ">=3.5"
 
 [package.extras]
-test = ["pytest", "flake8", "mypy"]
+test = ["flake8", "mypy", "pytest"]
 
 [[package]]
 name = "sphinxcontrib-qthelp"
@@ -874,7 +874,7 @@ optional = false
 python-versions = ">=3.5"
 
 [package.extras]
-lint = ["flake8", "mypy", "docutils-stubs"]
+lint = ["docutils-stubs", "flake8", "mypy"]
 test = ["pytest"]
 
 [[package]]
@@ -886,7 +886,7 @@ optional = false
 python-versions = ">=3.5"
 
 [package.extras]
-lint = ["flake8", "mypy", "docutils-stubs"]
+lint = ["docutils-stubs", "flake8", "mypy"]
 test = ["pytest"]
 
 [[package]]
@@ -942,8 +942,8 @@ optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*, <4"
 
 [package.extras]
-brotli = ["brotlicffi (>=0.8.0)", "brotli (>=1.0.9)", "brotlipy (>=0.6.0)"]
-secure = ["pyOpenSSL (>=0.14)", "cryptography (>=1.3.4)", "idna (>=2.0.0)", "certifi", "urllib3-secure-extra", "ipaddress"]
+brotli = ["brotli (>=1.0.9)", "brotlicffi (>=0.8.0)", "brotlipy (>=0.6.0)"]
+secure = ["certifi", "cryptography (>=1.3.4)", "idna (>=2.0.0)", "ipaddress", "pyOpenSSL (>=0.14)", "urllib3-secure-extra"]
 socks = ["PySocks (>=1.5.6,!=1.5.7,<2.0)"]
 
 [[package]]
@@ -981,8 +981,8 @@ optional = false
 python-versions = ">=3.7"
 
 [package.extras]
-docs = ["sphinx (>=3.5)", "jaraco.packaging (>=9)", "rst.linker (>=1.9)", "furo", "jaraco.tidelift (>=1.4)"]
-testing = ["pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-flake8", "flake8 (<5)", "pytest-cov", "pytest-enabler (>=1.3)", "jaraco.itertools", "func-timeout", "jaraco.functools", "more-itertools", "pytest-black (>=0.3.7)", "pytest-mypy (>=0.9.1)"]
+docs = ["furo", "jaraco.packaging (>=9)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)"]
+testing = ["flake8 (<5)", "func-timeout", "jaraco.functools", "jaraco.itertools", "more-itertools", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=1.3)", "pytest-flake8", "pytest-mypy (>=0.9.1)"]
 
 [extras]
 docs = ["Sphinx", "sphinx-autodoc-typehints", "sphinx-rtd-theme", "numpydoc", "sphinx-click"]
@@ -1484,8 +1484,8 @@ pillow = [
     {file = "Pillow-9.3.0.tar.gz", hash = "sha256:c935a22a557a560108d780f9a0fc426dd7459940dc54faa49d83249c8d3e760f"},
 ]
 platformdirs = [
-    {file = "platformdirs-2.5.2-py3-none-any.whl", hash = "sha256:027d8e83a2d7de06bbac4e5ef7e023c02b863d7ea5d079477e722bb41ab25788"},
-    {file = "platformdirs-2.5.2.tar.gz", hash = "sha256:58c8abb07dcb441e6ee4b11d8df0ac856038f944ab98b7be6b27b2a3c7feef19"},
+    {file = "platformdirs-2.5.3-py3-none-any.whl", hash = "sha256:0cb405749187a194f444c25c82ef7225232f11564721eabffc6ec70df83b11cb"},
+    {file = "platformdirs-2.5.3.tar.gz", hash = "sha256:6e52c21afff35cb659c6e52d8b4d61b9bd544557180440538f255d9382c8cbe0"},
 ]
 pluggy = [
     {file = "pluggy-1.0.0-py2.py3-none-any.whl", hash = "sha256:74134bbf457f031a36d68416e1509f34bd5ccc019f0bcc952c7b909d06b37bd3"},