From 3352277392ed36080b49df8875e098568991b4bc Mon Sep 17 00:00:00 2001
From: Clara <57916928+clarabakker@users.noreply.github.com>
Date: Mon, 30 Oct 2023 20:43:02 -0400
Subject: [PATCH 1/2] manage h5file I/O, convert to poetry, update versions of
 all libraries, adjust test for new output

---
 hic2cool/hic2cool_updates.py |   2 +-
 hic2cool/hic2cool_utils.py   |  52 +--
 poetry.lock                  | 686 +++++++++++++++++++++++++++++++++++
 pyproject.toml               |  41 +++
 setup.cfg                    |   2 -
 setup.py                     |  54 ---
 test.py                      |   7 +-
 7 files changed, 757 insertions(+), 87 deletions(-)
 create mode 100644 poetry.lock
 create mode 100644 pyproject.toml
 delete mode 100644 setup.cfg
 delete mode 100644 setup.py

diff --git a/hic2cool/hic2cool_updates.py b/hic2cool/hic2cool_updates.py
index c1465fe..794608d 100644
--- a/hic2cool/hic2cool_updates.py
+++ b/hic2cool/hic2cool_updates.py
@@ -118,7 +118,7 @@ def add_v3_attrs(h5_data, res=None):
                 add_v3_attrs(h5_file['resolutions'][res], res=res)
         else:
             add_v3_attrs(h5_file)
-       h5_file.close()
+        h5_file.close()
 
 
 def update_mcool_schema_v2(writefile):
diff --git a/hic2cool/hic2cool_utils.py b/hic2cool/hic2cool_utils.py
index 5f9ab9e..fac8499 100755
--- a/hic2cool/hic2cool_utils.py
+++ b/hic2cool/hic2cool_utils.py
@@ -38,8 +38,8 @@
 from ._version import __version__
 from .hic2cool_updates import prepare_hic2cool_updates
 from .hic2cool_config import *
-from multiprocessing import Pool
-#from multiprocessing import Process, Manager
+#import dill
+from multiprocess import Pool
 
 # input vs. raw_input for python 2/3
 try:
@@ -310,8 +310,8 @@ def read_normalization_vector(f, buf, entry):
     return np.frombuffer(buf, dtype=np.dtype('<d'), count=nValues, offset=filepos+4)
 
 
-def parse_hic(req, pool, nproc, chr_key, unit, binsize, pair_footer_info,
-              chr_offset_map, chr_bins, used_chrs, show_warnings):
+def parse_hic(infile, pool, nproc, chr_key, unit, binsize, pair_footer_info,
+              chr_offset_map, chr_bins, used_chrs, show_warnings, mmap_buf, req_ar):
     """
     Adapted from the straw() function in the original straw package.
     Mainly, since all chroms are iterated over, the read_header and read_footer
@@ -321,13 +321,12 @@ def parse_hic(req, pool, nproc, chr_key, unit, binsize, pair_footer_info,
     generously provided by Nezar. Reads are buffered using mmap and a lot of
     functions were condensed
     """
-    global mmap_buf
     # join chunk is an np array
     # that will contain the entire list of c1/c2 counts
     join_chunk = np.zeros(shape=0, dtype=CHUNK_DTYPE)
     if unit not in ["BP", "FRAG"]:
         error_string = "!!! ERROR. Unit specified incorrectly, must be one of <BP/FRAG>"
-        force_exit(error_string, req)
+        force_exit(error_string)
     c1 = int(chr_key.split('_')[0])
     c2 = int(chr_key.split('_')[1])
     try:
@@ -342,7 +341,8 @@ def parse_hic(req, pool, nproc, chr_key, unit, binsize, pair_footer_info,
         return join_chunk
     region_indices = [0, chr_bins[c1], 0, chr_bins[c2]]
     myFilePos = pair_footer_info[chr_key]
-    block_info, block_bins, block_cols = read_blockinfo(req, mmap_buf, myFilePos, unit, binsize)
+    with open(infile, 'rb') as req:
+        block_info, block_bins, block_cols = read_blockinfo(req, mmap_buf, myFilePos, unit, binsize)
     if len(block_info) >= nproc and nproc >= 2:
         mpi_result = [None] * nproc
         blocklen = len(block_info) // nproc
@@ -352,29 +352,28 @@ def parse_hic(req, pool, nproc, chr_key, unit, binsize, pair_footer_info,
                 block_end = len(block_info)
             else:
                 block_end = (mpi + 1) * blocklen
-            mpi_result[mpi] = pool.apply_async(build_counts_chunk, (mpi, c1, c2, block_info[block_start:block_end], chr_offset_map, region_indices,))
+            mpi_result[mpi] = pool.apply_async(build_counts_chunk, (mpi, c1, c2, block_info[block_start:block_end], chr_offset_map, region_indices, req_ar))
         result_all = []
         for mpi in range(0, nproc):
             mpi_result[mpi].wait()
             result_all.extend(mpi_result[mpi].get())
         return np.concatenate(result_all, axis=0)
     else:
-        result_all = build_counts_chunk(0, c1, c2, block_info, chr_offset_map, region_indices)
+        result_all = build_counts_chunk(0, c1, c2, block_info, chr_offset_map, region_indices, req_ar)
         return np.concatenate(result_all, axis=0)
     #return build_counts_chunk(nproc, c1, c2, block_info, chr_offset_map, region_indices)
 
 
-def build_counts_chunk(mpi, c1, c2, block_info, chr_offset_map, region_indices):
+def build_counts_chunk(mpi, c1, c2, block_info, chr_offset_map, region_indices, reqarr):
     """
     Takes the given block_info and find those bin_IDs/counts from the hic file,
     using them to build and return a chunk of counts
     """
     [binX0, binX1, binY0, binY1] = region_indices
     block_results = []
-    global reqarr
-    req = reqarr[mpi]
+    req_file = reqarr[mpi]
     for block_record in block_info:
-        records = read_block(req, block_record)
+        records = read_block(req_file, block_record)
         # skip empty records
         if not records.size:
             continue
@@ -391,7 +390,7 @@ def build_counts_chunk(mpi, c1, c2, block_info, chr_offset_map, region_indices):
     return block_results
 
 
-def initialize_res(outfile, req, buf, unit, chr_info, genome, metadata,
+def initialize_res(outfile, infile, buf, unit, chr_info, genome, metadata,
                    resolution, norm_info, multi_res, show_warnings):
     """
     Use various information to initialize a cooler file in HDF5 format. Tables
@@ -427,7 +426,7 @@ def initialize_res(outfile, req, buf, unit, chr_info, genome, metadata,
         # bins
         bin_table, chr_offsets, by_chr_bins, by_chr_offset_map = create_bins(chr_info, resolution)
         grp = h5resolution.create_group('bins')
-        write_bins(grp, req, buf, unit, resolution, chr_names, bin_table, by_chr_bins, norm_info, show_warnings)
+        write_bins(grp, infile, buf, unit, resolution, chr_names, bin_table, by_chr_bins, norm_info, show_warnings)
         n_bins = len(bin_table)
         # indexes (just initialize bin1offets)
         grp = h5resolution.create_group('indexes')
@@ -514,7 +513,7 @@ def create_bins(chrs, binsize):
     return np.array(bins_array), np.array(offsets), by_chr_bins, by_chr_offsets
 
 
-def write_bins(grp, req, buf, unit, res, chroms, bins, by_chr_bins, norm_info, show_warnings):
+def write_bins(grp, infile, buf, unit, res, chroms, bins, by_chr_bins, norm_info, show_warnings):
     """
     Write the bins table, which has columns: chrom, start (in bp), end (in bp),
     and one column for each normalization type, named for the norm type.
@@ -557,11 +556,12 @@ def write_bins(grp, req, buf, unit, res, chroms, bins, by_chr_bins, norm_info, s
                 WARN = True
                 if show_warnings:
                     print_stderr('!!! WARNING. Normalization vector %s does not exist for chr idx %s.'
-                          % (norm, chr_idx))
+                        % (norm, chr_idx))
                 # add a vector of nan's for missing vectors
                 norm_data.extend([np.nan]*chr_bin_end)
                 continue
-            norm_vector = read_normalization_vector(req, buf, norm_key)
+            with open(infile, "rb") as req:    
+                norm_vector = read_normalization_vector(req, buf, norm_key)
             # NOTE: possible issue to look into
             # norm_vector returned by read_normalization_vector has an extra
             # entry at the end (0.0) that is never used and causes the
@@ -575,7 +575,7 @@ def write_bins(grp, req, buf, unit, res, chroms, bins, by_chr_bins, norm_info, s
             error_str = (
                 '!!! ERROR. Length of normalization vector %s does not match the'
                 ' number of bins.\nThis is likely a problem with the hic file' % (norm))
-            force_exit(error_str, req)
+            force_exit(error_str)
         grp.create_dataset(
             norm,
             shape=(len(norm_data),),
@@ -669,6 +669,7 @@ def write_pixels_chunk(outfile, resolution, chunks, multi_res):
             prev_size = dataset.shape[0]
             dataset.resize(prev_size + nnz, axis=0)
             dataset[prev_size:] = chunks[set_name]
+        h5file.close()
 
 
 def finalize_resolution_cool(outfile, resolution, multi_res):
@@ -691,6 +692,7 @@ def finalize_resolution_cool(outfile, resolution, multi_res):
         # update attributes with nnz
         info = {'nnz': nnz}
         h5resolution.attrs.update(info)
+        h5file.close()
 
 
 def rlencode(array, chunksize=None):
@@ -824,6 +826,7 @@ def run_hic2cool_updates(updates, infile, writefile):
             h5_file.attrs['generated-by'] = generated_by
             h5_file.attrs['update-date'] = update_data
             print('... Updated metadata')
+        h5_file.close()
     print('### Finished! Output written to: %s' % writefile)
 
 
@@ -850,11 +853,9 @@ def hic2cool_convert(infile, outfile, resolution=0, nproc=1, show_warnings=False
     global WARN
     WARN = False
     req = open(infile, 'rb')
-    global reqarr
     reqarr = []
     for i in range(0, nproc):
         reqarr.append(open(infile, 'rb'))
-    global mmap_buf
     mmap_buf = mmap.mmap(req.fileno(), 0, access=mmap.ACCESS_READ)
     used_chrs, resolutions, masteridx, genome, metadata = read_header(req)
     pair_footer_info, expected, factors, norm_info = read_footer(req, mmap_buf, masteridx)
@@ -910,13 +911,13 @@ def hic2cool_convert(infile, outfile, resolution=0, nproc=1, show_warnings=False
             force_exit(error_string, req)
         if WARN:
             print_stderr('!!! WARNING: removed pre-existing file: %s' % (outfile))
-
+    req.close()
     print('### Converting')
     pool = Pool(processes=nproc)
     for binsize in use_resolutions:
         t_start = time.time()
         # initialize cooler file. return per resolution bin offset maps
-        chr_offset_map, chr_bins = initialize_res(outfile, req, mmap_buf, unit, used_chrs,
+        chr_offset_map, chr_bins = initialize_res(outfile, infile, mmap_buf, unit, used_chrs,
                                         genome, metadata, binsize, norm_info, multi_res, show_warnings)
         covered_chr_pairs = []
         for chr_a in used_chrs:
@@ -933,9 +934,9 @@ def hic2cool_convert(infile, outfile, resolution=0, nproc=1, show_warnings=False
                 # and c2-c1 reciprocally
                 if chr_key in covered_chr_pairs:
                     continue
-                tmp_chunk = parse_hic(req, pool, nproc, chr_key, unit, binsize,
+                tmp_chunk = parse_hic(infile, pool, nproc, chr_key, unit, binsize,
                                       pair_footer_info, chr_offset_map, chr_bins,
-                                      used_chrs, show_warnings)
+                                      used_chrs, show_warnings, mmap_buf, reqarr)
                 total_chunk = np.concatenate((total_chunk, tmp_chunk), axis=0)
                 del tmp_chunk
                 covered_chr_pairs.append(chr_key)
@@ -948,7 +949,6 @@ def hic2cool_convert(infile, outfile, resolution=0, nproc=1, show_warnings=False
         elapsed_parse = t_parse - t_start
         if not silent:
             print('... Resolution %s took: %s seconds.' % (binsize, elapsed_parse))
-    req.close()
     for i in range(0, nproc):
         reqarr[i].close()
     pool.close()
diff --git a/poetry.lock b/poetry.lock
new file mode 100644
index 0000000..73b4397
--- /dev/null
+++ b/poetry.lock
@@ -0,0 +1,686 @@
+# This file is automatically @generated by Poetry 1.6.1 and should not be changed by hand.
+
+[[package]]
+name = "asciitree"
+version = "0.3.3"
+description = "Draws ASCII trees."
+optional = false
+python-versions = "*"
+files = [
+    {file = "asciitree-0.3.3.tar.gz", hash = "sha256:4aa4b9b649f85e3fcb343363d97564aa1fb62e249677f2e18a96765145cc0f6e"},
+]
+
+[[package]]
+name = "click"
+version = "8.1.7"
+description = "Composable command line interface toolkit"
+optional = false
+python-versions = ">=3.7"
+files = [
+    {file = "click-8.1.7-py3-none-any.whl", hash = "sha256:ae74fb96c20a0277a1d615f1e4d73c8414f5a98db8b799a7931d1582f3390c28"},
+    {file = "click-8.1.7.tar.gz", hash = "sha256:ca9853ad459e787e2192211578cc907e7594e294c7ccc834310722b41b9ca6de"},
+]
+
+[package.dependencies]
+colorama = {version = "*", markers = "platform_system == \"Windows\""}
+
+[[package]]
+name = "colorama"
+version = "0.4.6"
+description = "Cross-platform colored terminal text."
+optional = false
+python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,!=3.6.*,>=2.7"
+files = [
+    {file = "colorama-0.4.6-py2.py3-none-any.whl", hash = "sha256:4f1d9991f5acc0ca119f9d443620b77f9d6b33703e51011c16baf57afb285fc6"},
+    {file = "colorama-0.4.6.tar.gz", hash = "sha256:08695f5cb7ed6e0531a20572697297273c47b8cae5a63ffc6d6ed5c201be6e44"},
+]
+
+[[package]]
+name = "cooler"
+version = "0.9.3"
+description = "Sparse binary format for genomic interaction matrices."
+optional = false
+python-versions = ">=3.6"
+files = [
+    {file = "cooler-0.9.3-py3-none-any.whl", hash = "sha256:a52584e8df0f2ff7187f03cfee2dc4d94d85c5c17dcd90c91c946b7c7532441c"},
+    {file = "cooler-0.9.3.tar.gz", hash = "sha256:21eee066d6fa30185cd21b0ead94beb341a9fb974bd3190ee22627424a040b63"},
+]
+
+[package.dependencies]
+asciitree = "*"
+click = ">=7"
+cytoolz = "*"
+h5py = ">=2.5"
+multiprocess = "*"
+numpy = ">=1.9"
+pandas = ">1.0"
+pyfaidx = "*"
+pyyaml = "*"
+scipy = ">=0.16"
+simplejson = "*"
+
+[package.extras]
+complete = ["biopython", "dask[array,dataframe]", "ipytree (>=0.2.2)", "ipywidgets (>=8.0.0)", "matplotlib", "psutil", "pypairix", "pysam"]
+dev = ["cooler[complete,test]"]
+docs = ["autodocsumm", "m2r", "recommonmark", "sphinx (>=1.6)", "sphinx-autobuild", "sphinx-rtd-theme"]
+test = ["coverage[toml]", "isort", "pytest", "pytest-cov", "ruff"]
+
+[[package]]
+name = "cytoolz"
+version = "0.12.2"
+description = "Cython implementation of Toolz: High performance functional utilities"
+optional = false
+python-versions = ">=3.6"
+files = [
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+    {file = "simplejson-3.19.2-cp39-cp39-win32.whl", hash = "sha256:4edcd0bf70087b244ba77038db23cd98a1ace2f91b4a3ecef22036314d77ac23"},
+    {file = "simplejson-3.19.2-cp39-cp39-win_amd64.whl", hash = "sha256:aad7405c033d32c751d98d3a65801e2797ae77fac284a539f6c3a3e13005edc4"},
+    {file = "simplejson-3.19.2-py3-none-any.whl", hash = "sha256:bcedf4cae0d47839fee7de344f96b5694ca53c786f28b5f773d4f0b265a159eb"},
+    {file = "simplejson-3.19.2.tar.gz", hash = "sha256:9eb442a2442ce417801c912df68e1f6ccfcd41577ae7274953ab3ad24ef7d82c"},
+]
+
+[[package]]
+name = "six"
+version = "1.16.0"
+description = "Python 2 and 3 compatibility utilities"
+optional = false
+python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*"
+files = [
+    {file = "six-1.16.0-py2.py3-none-any.whl", hash = "sha256:8abb2f1d86890a2dfb989f9a77cfcfd3e47c2a354b01111771326f8aa26e0254"},
+    {file = "six-1.16.0.tar.gz", hash = "sha256:1e61c37477a1626458e36f7b1d82aa5c9b094fa4802892072e49de9c60c4c926"},
+]
+
+[[package]]
+name = "toolz"
+version = "0.12.0"
+description = "List processing tools and functional utilities"
+optional = false
+python-versions = ">=3.5"
+files = [
+    {file = "toolz-0.12.0-py3-none-any.whl", hash = "sha256:2059bd4148deb1884bb0eb770a3cde70e7f954cfbbdc2285f1f2de01fd21eb6f"},
+    {file = "toolz-0.12.0.tar.gz", hash = "sha256:88c570861c440ee3f2f6037c4654613228ff40c93a6c25e0eba70d17282c6194"},
+]
+
+[[package]]
+name = "tzdata"
+version = "2023.3"
+description = "Provider of IANA time zone data"
+optional = false
+python-versions = ">=2"
+files = [
+    {file = "tzdata-2023.3-py2.py3-none-any.whl", hash = "sha256:7e65763eef3120314099b6939b5546db7adce1e7d6f2e179e3df563c70511eda"},
+    {file = "tzdata-2023.3.tar.gz", hash = "sha256:11ef1e08e54acb0d4f95bdb1be05da659673de4acbd21bf9c69e94cc5e907a3a"},
+]
+
+[[package]]
+name = "zipp"
+version = "3.17.0"
+description = "Backport of pathlib-compatible object wrapper for zip files"
+optional = false
+python-versions = ">=3.8"
+files = [
+    {file = "zipp-3.17.0-py3-none-any.whl", hash = "sha256:0e923e726174922dce09c53c59ad483ff7bbb8e572e00c7f7c46b88556409f31"},
+    {file = "zipp-3.17.0.tar.gz", hash = "sha256:84e64a1c28cf7e91ed2078bb8cc8c259cb19b76942096c8d7b84947690cabaf0"},
+]
+
+[package.extras]
+docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (<7.2.5)", "sphinx (>=3.5)", "sphinx-lint"]
+testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-ignore-flaky", "pytest-mypy (>=0.9.1)", "pytest-ruff"]
+
+[metadata]
+lock-version = "2.0"
+python-versions = ">=3.8,<3.10"
+content-hash = "6353aafab14e8a621d082c00d91b65e47fb93ff9773f34727baa911e42116a27"
diff --git a/pyproject.toml b/pyproject.toml
new file mode 100644
index 0000000..a5951bf
--- /dev/null
+++ b/pyproject.toml
@@ -0,0 +1,41 @@
+# Written by Carl Vitzthum with help from Soo Lee
+# This code was originally based off of the straw project by Neva C. Durand and
+# Yue Wu (https://github.com/theaidenlab/straw). The cooler file writing was
+# based off of much of the CLI code contained in this
+# repo: https://github.com/mirnylab/cooler.
+
+[tool.poetry]
+name = "hic2cool"
+version = "1.0.0"
+description = """Converter between hic files (from juicer) and single-resolution or multi-resolution cool files (for cooler).  Both hic and cool files describe Hi-C contact matrices. Intended to be lightweight, this can be used as an imported package or a stand-alone Python tool for command line conversion."""
+authors = ["Carl Vitzthum <carl.vitzthum@gmail.com>"]
+license = "MIT"
+readme = "README.md"
+repository = "https://github.com/4dn-dcic/hic2cool/"
+keywords = ["bioinformatics", "genomics", "hi-c", "juicer", "cooler", "contact-matrix", "file-format"]
+classifiers = [
+    "Programming Language :: Python :: 3",
+    "Development Status :: 4 - Beta",
+    "Intended Audience :: Developers",
+    "Intended Audience :: Science/Research",
+    "License :: OSI Approved :: MIT License",
+    "Operating System :: OS Independent",
+    "Topic :: Software Development :: Libraries :: Python Modules",
+    "Topic :: Scientific/Engineering :: Bio-Informatics"
+]
+include = []
+packages = [
+    { include="hic2cool", from="." }
+]
+
+[tool.poetry.dependencies]
+python = ">=3.8,<3.10"
+numpy = ">=1.9"
+scipy = ">=1.10.1"
+pandas = ">=1.0"
+h5py = ">=2.5.0"
+cooler = "0.9.3"
+
+[build-system]
+requires = ["poetry_core>=1.0.0"]
+build-backend = "poetry.core.masonry.api"
diff --git a/setup.cfg b/setup.cfg
deleted file mode 100644
index b88034e..0000000
--- a/setup.cfg
+++ /dev/null
@@ -1,2 +0,0 @@
-[metadata]
-description-file = README.md
diff --git a/setup.py b/setup.py
deleted file mode 100644
index 23297d7..0000000
--- a/setup.py
+++ /dev/null
@@ -1,54 +0,0 @@
-#!/usr/bin/env python
-# Written by Carl Vitzthum with help from Soo Lee
-# This code was originally based off of the straw project by Neva C. Durand and
-# Yue Wu (https://github.com/theaidenlab/straw). The cooler file writing was
-# based off of much of the CLI code contained in this
-# repo: https://github.com/mirnylab/cooler.
-
-import io
-from setuptools import setup
-from os import path
-
-this_directory = path.abspath(path.dirname(__file__))
-with io.open(path.join(this_directory, 'README.md'), encoding='utf-8') as f:
-    long_description = f.read()
-
-with open('requirements.txt') as f:
-    set_parsed = f.read().splitlines()
-requires = [req.strip() for req in set_parsed if 'git+' not in req]
-
-this_version = io.open(path.join(this_directory, "hic2cool/_version.py")).readlines()[-1].split()[-1].strip("\"'")
-
-setup(
-    name = "hic2cool",
-    version = this_version,
-    packages = ['hic2cool'],
-    description = """Converter between hic files (from juicer) and single-resolution or multi-resolution cool files (for cooler).  Both hic and cool files describe Hi-C contact matrices. Intended to be lightweight, this can be used as an imported package or a stand-alone Python tool for command line conversion.""",
-    long_description=long_description,
-    long_description_content_type='text/markdown',
-    url = "https://github.com/4dn-dcic/hic2cool",
-    download_url = "https://github.com/4dn-dcic/hic2cool/tarball/" + this_version,
-    author = "Carl Vitzthum",
-    author_email = "carl.vitzthum@gmail.com",
-    license = "MIT",
-    keywords = ["bioinformatics", "genomics", "hi-c", "juicer", "cooler", "contact-matrix", "file-format"],
-    install_requires = requires,
-    setup_requires = requires,
-    tests_require = requires,
-    test_suite = "test",
-    entry_points = {
-        'console_scripts': [
-             'hic2cool = hic2cool.__main__:main',
-        ]
-    },
-    classifiers = [
-        "Programming Language :: Python :: 3",
-        "Development Status :: 4 - Beta",
-        "Intended Audience :: Developers",
-        "Intended Audience :: Science/Research",
-        "License :: OSI Approved :: MIT License",
-        "Operating System :: OS Independent",
-        "Topic :: Software Development :: Libraries :: Python Modules",
-        "Topic :: Scientific/Engineering :: Bio-Informatics"
-    ]
-)
diff --git a/test.py b/test.py
index 110ee09..f328d0f 100644
--- a/test.py
+++ b/test.py
@@ -62,7 +62,7 @@ def get_norms_content_md5(self, fname, use_resolutions=None, bin_lens={}):
         Also return int bin length found in the file
         """
         str_val = ''
-        with h5py.File(fname) as h5:
+        with h5py.File(fname, 'r') as h5:
             if not use_resolutions:
                 use_resolutions = [r for r in h5['resolutions']]
             for res in use_resolutions:
@@ -81,11 +81,11 @@ def get_norms_content_md5(self, fname, use_resolutions=None, bin_lens={}):
 
     def test_convert(self):
         hic2cool_convert(self.infile_name, self.outfile_name_all)
-        assert os.stat(self.outfile_name_all).st_size == 6158552
+        assert os.stat(self.outfile_name_all).st_size == 6158040
 
     def test_convert_multiprocessing(self):
         hic2cool_convert(self.infile_name, self.outfile_name_all, 0, 2)
-        assert os.stat(self.outfile_name_all).st_size == 6158552
+        assert os.stat(self.outfile_name_all).st_size == 6158040
 
     def test_0_run_with_warnings(self):
         with captured_output() as (out, err):
@@ -331,7 +331,6 @@ def test_no_norms(self):
             for norm in NORMS:
                 self.assertTrue(norm not in res500kb_bins.keys())
 
-
 class TestRunUpdate(unittest.TestCase):
     infile_name = 'test_data/hic2cool_0.4.2_single_res.cool'
     outfile_name = 'test_data/OUT_new_version_single_res.cool'

From 46864a3162a7c46f3e93d15857faa050266d9939 Mon Sep 17 00:00:00 2001
From: Clara <57916928+clarabakker@users.noreply.github.com>
Date: Mon, 30 Oct 2023 21:06:32 -0400
Subject: [PATCH 2/2] remove commented line, unused requirements file

---
 hic2cool/hic2cool_utils.py | 1 -
 requirements.txt           | 5 -----
 2 files changed, 6 deletions(-)
 delete mode 100644 requirements.txt

diff --git a/hic2cool/hic2cool_utils.py b/hic2cool/hic2cool_utils.py
index fac8499..cbfa191 100755
--- a/hic2cool/hic2cool_utils.py
+++ b/hic2cool/hic2cool_utils.py
@@ -38,7 +38,6 @@
 from ._version import __version__
 from .hic2cool_updates import prepare_hic2cool_updates
 from .hic2cool_config import *
-#import dill
 from multiprocess import Pool
 
 # input vs. raw_input for python 2/3
diff --git a/requirements.txt b/requirements.txt
deleted file mode 100644
index c4d557c..0000000
--- a/requirements.txt
+++ /dev/null
@@ -1,5 +0,0 @@
-h5py>=2.8.0
-numpy>=1.10.1
-scipy
-pandas
-cooler>=0.8.5