3.x (#147)

* dbcan 3.x development (#141)

* move cli to the pkg

* add .editorconfig

* add pre-commit-config.yaml

* add .dockerignore

* reformat

* rm setup script and conf

* change ValueError to KeyError

* add readthedocs conf

* add .toml to manage the proj

* add sphinx docs

* .dockerignore

* add user guide doc

* simplify readme

* reorder authors

* :Update 4.1.0: 1. Update dbCAN 2. Harmonizing codes from Jinfang's updates

* fix small bugs

* update dbCAN version

* revise sha256 for 4.1.0

* add yml file to install environment for dbcan-protocol

* remove usage

* :add: readthedoc badge

* [fix] fix bug in meta.yaml

---------

Co-authored-by: HD Yi <[email protected]>

README.md

@@ -1,4 +1,5 @@
 [![dbcan](https://github.com/linnabrown/run_dbcan/actions/workflows/ci.yml/badge.svg?branch=master)](https://github.com/linnabrown/run_dbcan/actions/workflows/ci.yml)
+[![Documentation Status](https://readthedocs.org/projects/dbcan/badge/?version=latest)](https://dbcan.readthedocs.io/en/latest/?badge=latest)
 [![Package status](https://anaconda.org/bioconda/dbcan/badges/version.svg)](https://anaconda.org/bioconda/dbcan)
 [![GitHub license](https://img.shields.io/badge/license-GNU3.0-blue.svg)](https://github.com/linnabrown/run_dbcan/blob/master/LICENSE)
 [![Platform](https://anaconda.org/bioconda/dbcan/badges/platforms.svg)](https://anaconda.org/bioconda/dbcan/badges/platforms.svg)

conda-recipe/meta.yaml

@@ -6,56 +6,63 @@ package:
   version: {{ version }}
 
 source:
+  # the sha256 sum is generated by doing 
+  # wget -0- [URL] | shasum -a 256
   url: https://github.com/linnabrown/run_dbcan/releases/download/{{ version }}/dbcan-{{ version }}.tar.gz
-  sha256: 7e51b2a76018df39ec635f58a68b2e946a44cd4b1673906ed8ae947d68092573
+  sha256: cb0907eb10eb916bcf676c58f54e67a67dd4ed559152e5547bb44d071f063b8f
+
 build:
   number: 0
-  script: "{{ PYTHON }} -m pip install . -vv"
+  script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv"
   noarch: python
+  entry_points:
+    - run_dbcan = dbcan.cli.run_dbcan:cli_main
+    - cgc_standard2json = dbcan.cli.cgc_process_json:main
+    - syntenic_plot = dbcan.cli.syntenic_plot:main
+    - dbcan_utils = dbcan.utils.utils:main
+    - dbcan_plot = dbcan.utils.plots:main
+    - dbcan_asmfree = dbcan.utils.diamond_unassembly:main
+  run_exports:
+    - {{ pin_subpackage(name, max_pin="x") }}
 
 requirements:
   host:
-    - natsort
     - pip
-    - python
-    - setuptools
-    - setuptools_scm_git_archive
-
+    - python >=3.6
+    - hatchling
   run:
     - natsort
-    - python
+    - python >=3.6
     - diamond
     - hmmer
-    - blast
-    - pyhmmer
-    - Prokka
-    - megahit
-    - trim-galore
-    - bwa
-    - samtools
-    - bedtools
-    - seqkit
-    - kraken2
     - prodigal
     - scipy
     - psutil
     - numpy >1.19
     - biopython
     - pandas
-    - openpyxl
-    - matplotlib
+    - session-info
 
 test:
   imports:
     - dbcan
+  commands:
+    - run_dbcan --help
 
 about:
-  home: http://bcb.unl.edu/dbCAN2/
+  home: https://bcb.unl.edu/dbCAN2/
   dev_url: https://github.com/linnabrown/run_dbcan
-  license: GPLv3
+  license: GPL-3.0-or-later
+  license_family: GPL3
   license_file: LICENSE
-  summary: Standalone version of dbCAN annotation tool for automated CAZyme annotation
+  summary: "Standalone version of dbCAN annotation tool for automated CAZyme annotation"
+  doc_url: https://dbcan.readthedocs.io/en/latest/
 
 extra:
   recipe-maintainers:
-    - Le Huang
+    - linnabrown
+  identifiers:
+    - doi:10.1093/nar/gkx894
+    - doi:10.1093/nar/gky418
+    - doi:10.1093/nar/gkad328
+    - biotools:dbcan2