Update Saccharis (#51314)

* Add recipe for saccharis 2.0 dev18 build 1 to bioconda

* updated to use git tag

* updated to use a python package generated from setuptools build, with sha256 hash, and added --single-version-externally-managed --record=record.txt args to setup.py install as per bioconda test suite

* lowercased hash, since it's case-sensitive

* added filename as "fn: saccharis-{{ version }}.tar.gz"

* removed filename since bioconda considers it an error

* update url link

* update sha256

* remove unneeded comments

* remove tests which write files

* remove tests which write files, with comment

* add new release data to bioconda recipe

* change build number to zero to satisfy bioconda linter

* add blast dependency

* add run_exports breaking change behaviour

* change name to lowercase in run_exports

* fix spacing

* nesting issue

* remove nesting

* fix version spacing

* update to dev20

* update to dev20

* update to dev21

* fix >= sign

* increment build to fix small error

* update file hash and increment build

* revert 2.0.1 to working dev21 build

* upload 2.0.1 dev21 version with fixed database download

* upload 2.0.1 dev21 version with another database download fix

* increment build num

* increment build num

* increment build num

* update setuptools build requirements

* update setuptools build requirements

recipes/saccharis/meta.yaml

@@ -1,19 +1,20 @@
 {% set name = "SACCHARIS" %}
 {% set version = "2.0.1.dev21" %}
-{% set hash = "1e5c4bb35414d1421f4debcf0ecb53cd62a853b40a887486a44c2c7a8929b113" %}
+{% set hash = "327FCE45E7B50BF0C52064DA883CC4A21BCE183EBACF4C4A827FE2C5BE934CB3" %}
 
 
 package:
   name: "{{ name|lower }}"
   version: "{{ version }}"
 
 source:
-  url: https://github.com/saccharis/SACCHARIS_2/releases/download/v{{ version }}/saccharis-{{ version }}.tar.gz
+  #  url: https://github.com/saccharis/SACCHARIS_2/releases/download/v{{ version }}/saccharis-{{ version }}.tar.gz
+  url: https://github.com/saccharis/SACCHARIS_2/releases/download/v2.0.1.dev21/saccharis-2.0.1.dev21_2.tar.gz
   sha256: {{ hash|lower }}
 
 build:
   noarch: python
-  number: 0
+  number: 2
   script: {{ PYTHON }} setup.py install --single-version-externally-managed --record=record.txt
   preserve_egg_dir: True  # added because the entry points below seem to be causing a build error
   entry_points:
@@ -23,16 +24,20 @@ build:
     - saccharis.rename_user_file = saccharis.utils.UserFastaRename:cli_main
     - saccharis.prune_seqs = saccharis.ExtractAndPruneCAZymes:cli_prune_seqs
     - saccharis.screen_cazome = saccharis.ScreenUserFile:cli_cazome
-    - saccharis.show_family_categories = saccharis.utils.FamilyCategories:show_categories
+    - saccharis.show_family_categories = saccharis.utils.FamilyCategories:cli_show_categories
     - saccharis-gui = saccharis.gui.PipelineGUI:main
     - saccharis.config = saccharis.utils.AdvancedConfig:cli_config
-    - saccharis.update_db = saccharis.ExtractAndPruneCAZymes:update_hmms
+    - saccharis.update_db = saccharis.utils.DatabaseDownload:cli_update_hmms
   run_exports:
     - {{ pin_subpackage("saccharis", max_pin="x.x") }}
 
 requirements:
+  build:
+    - python
+    - setuptools
   host:
     - python >=3.6
+    - setuptools
     - pip
   run:
     - beautifulsoup4 >=4.11.1
@@ -70,14 +75,20 @@ test:
   commands:
     # pipe test output to null for these tests, per https://bioconda.github.io/contributor/guidelines.html#tests
     - saccharis -v > /dev/null
-    - saccharis.show_family_categories > /dev/null
-#    below tests need to be commented out for successful build on bioconda because there is no file write permission
-#    - saccharis.make_family_files
+    - saccharis.show_family_categories --help > /dev/null
+    - saccharis.make_family_files --help > /dev/null
+    - saccharis.add_family_category --help > /dev/null
+    - saccharis.rename_user_file --help > /dev/null
+    - saccharis.prune_seqs --help > /dev/null
+    - saccharis.screen_cazome --help > /dev/null
+    - saccharis.config --help > /dev/null
+    - saccharis.update_db --help > /dev/null
 
 about:
   home: https://github.com/saccharis/SACCHARIS_2
   dev_url: https://github.com/saccharis/SACCHARIS_2
-  description: Bioinformatics pipeline to automate phylogenetic analysis of CAZyme families in FASTA sequences via creation of phylogenetic trees.
+  description: Bioinformatics pipeline to automate phylogenetic analysis of CAZyme families in FASTA sequences via
+    creation of phylogenetic trees.
   license: GPL-3.0-or-later
   license_family: GPL3
   license_file: LICENSE