chore: clean-up repo (#196)

* chore: removed sm file

* chore: removed sh requirement

* chore: removed natsort

* chore: removed more-itertools

* chore: removed pyyamml

* chore: updated environment.yml minimum versions

* docs: updated readme docs badge

* docs: updated readme notes

* chore: removed setup.cfg

* fix: added dynamic dependencies to pyproject.toml

* fix: added back more-itertools requirement

* chore(packaging): added entry point

* chore: updated pyarrow requirement

* feat: added full install option

* chore: updated requirements

* docs: "full" install instruction added to docs

* fix(docs): cluster_config.md missing from index

* chore: workflow now installs with "full" option

* fix: cookiecutter missing from requirements

* fix: cookiecutter added to environment.yml

* chore(tests): remove old tests

* fix(packaging): lowered pyarrow max version

* feat(api): removed deduplicate and digest

* feat: deduplicate now a single command

* feat(cli-fastq): removed deduplicate subcommands

* feat(cli): corrected fastq dedup for cct

* feat(cli-fastq-dedup): updated dedup function

* feat: corrected stats for digest_fastq

* fix: corrected genome digestion tests

* fix: corrected fastq deduplicate

* chore: capcruncher tools and tracknado now deps

* fix(tests): corrected deduplicate test

* fix(fastq_deduplicate): removed old code

* fix: corrected digestion stats output

* chore: capcruncher_tools now >= 0.1.8

* feat: integrated capcruncher_tools count

* fix:  removed unwanted code

* fix: typo in output path

* fix: corrected small integration pipeline issues

* chore(pipeline): not checking for cct install

* fix: corrected digestion read_stats

* chore: cct to >= 0.1.9

* ci: added macos to test os

* fix: removed cct specific branch in stats

* fix: added os specific dependency install

* ci: removed ray from environment.
Not on conda for macos

* fix: removed fastq duplicate testing

* fix(ci): installing coreutils for macos

* fix(macos): using gsplit and gzcat vs split/zcat

* fix(fastq digest): missing restriction site

Using get_restriction_site() to correct

* fix(genome-digestion): added rs identification

* fix(tests): corrected deduplication test

* fix(ci): ignoring macos for now

* fix(tests): removed concurrent futures

* feat(fastq): make output directory first

* chore(coverage): delete files to boost coverage

.github/workflows/CI.yml

@@ -7,9 +7,10 @@ env:
 
 jobs:
   install-and-test:
-    runs-on: ubuntu-latest
+    runs-on: ${{ matrix.os }}
     strategy:
       matrix:
+        os: [ubuntu-latest]
         python-version: ["3.10"]
 
     steps:
@@ -20,11 +21,17 @@ jobs:
         with:
           python-version: ${{ matrix.python-version }}
 
-      - name: Install OS dependencies
+      - name: Install Linux dependencies
+        if: matrix.os == 'ubuntu-latest'
         run: |
           sudo apt-get update
           sudo apt-get install libcurl4-openssl-dev
 
+      # - name: Install Mac dependencies
+      #   if: matrix.os == 'macos-latest'
+      #   run: |
+      #     brew install curl-openssl coreutils
+
       - name: Restore bowtie2 cache
         uses: actions/cache@v3
         with:
@@ -69,7 +76,7 @@ jobs:
       - name: Install the package
         shell: bash -el {0}
         run: |
-          pip install .[stats,plotting,experimental]
+          pip install .[full]
 
       - name: Test with pytest and generate report
         shell: bash -el {0}

README.md

@@ -1,23 +1,26 @@
 # CapCruncher
 
-[![Documentation](https://github.com/sims-lab/CapCruncher/actions/workflows/docs.yml/badge.svg?branch=master)](https://github.com/sims-lab/CapCruncher/actions/workflows/docs.yml)
+[![Documentation](https://github.com/sims-lab/CapCruncher/actions/workflows/docs.yml/badge.svg?branch=master)](https://sims-lab.github.io/CapCruncher/)
 [![Codecov](https://codecov.io/gh/sims-lab/CapCruncher/branch/master/graph/badge.svg?token=RHIGNMGX09)](https://codecov.io/gh/sims-lab/CapCruncher)
 [![Anaconda-Server Badge](https://anaconda.org/bioconda/capcruncher/badges/version.svg)](https://anaconda.org/bioconda/capcruncher)
 [![Anaconda-Server Badge License](https://anaconda.org/bioconda/capcruncher/badges/license.svg)](https://anaconda.org/bioconda/capcruncher)
 [![DOI](https://zenodo.org/badge/224631087.svg)](https://zenodo.org/badge/latestdoi/224631087)
 [![Downloads](https://pepy.tech/badge/capcruncher)](https://pepy.tech/project/capcruncher)
 
-![CapCruncher Logo](https://github.com/sims-lab/CapCruncher/blob/68a91cea502a8623c71919c5f8d85febd6acef06/docs/img/capcruncher_logo.png)
+![CapCruncher Logo](https://raw.githubusercontent.com/sims-lab/CapCruncher/master/docs/img/capcruncher_logo.png)
 
 The CapCruncher package is designed to process Capture-C, Tri-C and Tiled-C data. Unlike other pipelines that are designed to process Hi-C or Capture-HiC data, the filtering steps in CapCruncher are specifically optimized for these datasets. The package consists of a configurable data processing pipeline and a supporting command line interface to enable fine-grained control over the analysis. The pipeline is fast, robust and scales from a single workstation to a large HPC cluster. It is designed to be run on an HPC cluster and can be configured to use a variety of package management systems, such as conda and singularity. For more information, see the [documentation](https://sims-lab.github.io/CapCruncher/).
 
-**Note:** The current version of CapCruncher is in beta. Please report any issues you encounter to the [issue tracker](https://github.com/sims-lab/CapCruncher/issues/new/choose)
+> **Note:**
+> The current version of CapCruncher is in beta. Please report any issues you encounter to the [issue tracker](https://github.com/sims-lab/CapCruncher/issues/new/choose)
 
 ## Quick Start
 
 ### Installation
 
-**Warning:** CapCruncher is currently only availible for linux with MacOS support planned in the future.
+> **Warning:**
+>
+> CapCruncher is currently only availible for linux with MacOS support planned in the future.
 
 CapCruncher is available on conda and PyPI. To install the latest version, run:
 
@@ -77,15 +80,17 @@ capcruncher pipeline --cores <NUMBER OF CORES TO USE>
 capcruncher pipeline --cores 8 --profile slurm --use-singularity
 ```
 
-**Note:** In order to avoid disconnecting from the cluster, it is recommended to run the pipeline in a [tmux](https://linuxize.com/post/getting-started-with-tmux/) session. Alternatively, [nohup](https://linuxize.com/post/linux-nohup-command/) can be used to run the pipeline in the background. For example:
-
-``` bash
-# tmux example
-tmux new -s capcruncher
-capcruncher pipeline --cores 8 --profile slurm --use-singularity
-
-# nohup example
-nohup capcruncher pipeline --cores 8 --profile slurm --use-singularity &
-```
+> **Note:**
+> In order to avoid disconnecting from the cluster, it is recommended to run the pipeline in a [tmux](https://linuxize.com/post/getting-started-with-tmux/)
+> session. Alternatively, [nohup](https://linuxize.com/post/linux-nohup-command/) can be used to run the pipeline in the background. For example:
+>
+> ``` bash
+> # tmux example
+>tmux new -s capcruncher
+> capcruncher pipeline --cores 8 --profile slurm --use-singularity
+>
+># nohup example
+>nohup capcruncher pipeline --cores 8 --profile slurm --use-singularity &
+>```
 
 See the [pipeline guide](https://sims-lab.github.io/CapCruncher/pipeline/) for more detailed instructions.