From cdce7f93ad831142a6d6e1cf75181bd5b7ba1973 Mon Sep 17 00:00:00 2001 From: SooLee Date: Thu, 26 Mar 2020 15:21:00 +0000 Subject: [PATCH 1/5] loosened dependency versions --- requirements.txt | 12 +++++++----- setup.py | 13 +++---------- 2 files changed, 10 insertions(+), 15 deletions(-) diff --git a/requirements.txt b/requirements.txt index d7e701b..1dca881 100644 --- a/requirements.txt +++ b/requirements.txt @@ -1,5 +1,7 @@ -h5py==2.8.0 -pandas==0.24.2 -numpy==1.16.3 -scipy==1.2.1 -cooler==0.8.5 +cython>=0.29.15 +cytoolz>=0.10.1 +h5py>=2.8.0 +pandas>=0.24.2 +numpy>=1.16.3 +scipy>=1.2.1 +cooler>=0.8.5 diff --git a/setup.py b/setup.py index b97f0ab..23297d7 100644 --- a/setup.py +++ b/setup.py @@ -13,16 +13,9 @@ with io.open(path.join(this_directory, 'README.md'), encoding='utf-8') as f: long_description = f.read() -# dependencies must be handled carefully for py2 and py3 compatibility -# specifically, scipy==1.3.0 -requires = [ - 'h5py>=2.8.0', - 'numpy>=1.10.1,<=1.16.3', - 'scipy<=1.2.1', - 'pandas<=0.24.2', - 'cooler>=0.8.5' - -] +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("\"'") From 9276f09a7bfd5c9d662c219bf6c647f0373ad964 Mon Sep 17 00:00:00 2001 From: SooLee Date: Fri, 27 Mar 2020 14:42:42 +0000 Subject: [PATCH 2/5] requirements the same as before --- requirements.txt | 8 +++----- 1 file changed, 3 insertions(+), 5 deletions(-) diff --git a/requirements.txt b/requirements.txt index 1dca881..1c9a66f 100644 --- a/requirements.txt +++ b/requirements.txt @@ -1,7 +1,5 @@ -cython>=0.29.15 -cytoolz>=0.10.1 h5py>=2.8.0 -pandas>=0.24.2 -numpy>=1.16.3 -scipy>=1.2.1 +numpy>=1.10.1,<=1.16.3 +scipy<=1.2.1 +pandas<=0.24.2 cooler>=0.8.5 From 0173b96a4079d443a4ae8cf2f9d0baabef88b24a Mon Sep 17 00:00:00 2001 From: SooLee Date: Fri, 27 Mar 2020 15:03:30 +0000 Subject: [PATCH 3/5] version update --- hic2cool/_version.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/hic2cool/_version.py b/hic2cool/_version.py index 777f190..8088f75 100644 --- a/hic2cool/_version.py +++ b/hic2cool/_version.py @@ -1 +1 @@ -__version__ = "0.8.0" +__version__ = "0.8.1" From 014c7ddc292fa2e43d6a3f2997437fb1da2630c5 Mon Sep 17 00:00:00 2001 From: SooLee Date: Fri, 27 Mar 2020 15:06:17 +0000 Subject: [PATCH 4/5] updated README --- README.md | 22 +++++++--------------- 1 file changed, 7 insertions(+), 15 deletions(-) diff --git a/README.md b/README.md index d888516..a7ca5cc 100644 --- a/README.md +++ b/README.md @@ -17,6 +17,11 @@ The hic parsing code is based off the [straw project](https://github.com/theaide $ pip install hic2cool ``` +You can also download the code directly and run the setup yourself. +``` +$ python setup.py install +``` + Once the package is installed, the main method is hic2cool_convert. It takes the same parameters as hic2cool.py, described in the next section. Example usage in a Python script is shown below or in test.py. ``` from hic2cool import hic2cool_convert @@ -31,21 +36,6 @@ The main use of hic2cool is converting between filetypes using `hic2cool convert $ hic2cool convert -r -p ``` -You can also download the code directly and run the setup yourself. First ensure that dependencies are installed: -``` -$ pip install -r requirements.txt -``` - -You can alternatively build the hic2cool package with: -``` -$ python setup.py install -``` - -Then, execute the Python code from the root directory with: -``` -$ python -m hic2cool convert -r -p -``` - ### Arguments for hic2cool convert **infile** is a .hic input file. @@ -128,6 +118,8 @@ You may also provide the optional `-e` flag, which will cause the mitchondrial c ## Changelog +### 0.8.1 +* `setup.py` takes dependencies directly from `requirements.txt` (`requirements.txt` updated to match `setup.py`) ### 0.8.0 * multiprocessing support for convert * change in usage of convert API due to the addition of the `nproc` option From ae153f29d2a0ad2e8e8bc88beede563d04b932d0 Mon Sep 17 00:00:00 2001 From: SooLee Date: Fri, 27 Mar 2020 15:26:51 +0000 Subject: [PATCH 5/5] added setuptools version guidelines to readme --- README.md | 1 + 1 file changed, 1 insertion(+) diff --git a/README.md b/README.md index a7ca5cc..cf52e06 100644 --- a/README.md +++ b/README.md @@ -19,6 +19,7 @@ $ pip install hic2cool You can also download the code directly and run the setup yourself. ``` +# setuptools >=42 is recommended $ python setup.py install ```