Use click (fixes #76)

.readthedocs.yml

@@ -1,16 +1,21 @@
 version: 2
 sphinx:
     configuration: doc/conf.py
+    builder: html
 
-
-formats: all
-
+# Set the version of Python and other tools you might need
+build:
+  os: ubuntu-22.04
+  tools:
+      python: "3.10"
+
+
+formats: []
 python:
-    version: 3.8
     install:
-        - requirements: doc/requirements.txt
         - method: pip
           path: .
+        - requirements: doc/requirements.txt
 
 # if present, this section is used and python section ignored before sphinx is built
 #conda:

README.rst

@@ -253,6 +253,10 @@ Changelog
 ========= ======================================================================
 Version   Description
 ========= ======================================================================
+0.16.0    * scripts now use click instead of argparse
+          * All Options classes have now an equivalent using click.
+            For example GeneralOptions has a class ClickGeneralOptions.
+            The GeneralOptions is kept for now for back compatibility
 0.15.0    * remove useless code (readme, description) related to old rules
           * requirements.txt renamed in tools.txt to store the required tools to 
             run a pipeline. 

pyproject.toml

@@ -6,7 +6,7 @@ build-backend = "poetry.core.masonry.api"
 #maintainer ?#maintainer email
 [tool.poetry]
 name = "sequana_pipetools"
-version = "0.15.0"
+version = "0.16.0"
 description = "A set of tools to help building or using Sequana pipelines"
 authors = ["Sequana Team"]
 license = "BSD-3"
@@ -33,11 +33,11 @@ packages = [
 ]
 
 [tool.poetry.dependencies]
-python = ">=3.8"
+python = ">=3.8,<4.0"
 deprecated = ">=1.2.13"
 easydev = ">=0.12.1"
 parse = ">=1.19.0"
-"ruamel.yaml" = ">=0.17.32"
+"ruamel.yaml" = ">=0.18.5"
 packaging = ">=23.1"
 pykwalify = ">=1.8"
 importlib_resources = ">=5.4.0"
@@ -46,18 +46,21 @@ aiohttp = ">=3.8.4"
 tqdm = ">=4.65"
 charset-normalizer = "^2"
 versionix = ">=0.2.0"
+rich-click = "^1.7.1"
 
 
 [tool.poetry.scripts]
 sequana_completion = "sequana_pipetools.scripts.completion:main"
 sequana_slurm_status = "sequana_pipetools.scripts.slurm:main"
+sequana_pipetools = "sequana_pipetools.scripts.main:main"
 
 
 [tool.poetry.group.dev.dependencies]
 black = "^23.7.0"
 pytest = "^7.4.0"
 mock = "^5.1.0"
 pytest-mock = "^3.11.1"
-sequana-fastqc = "^1.7.1"
+sequana-rnaseq = "^0.18.0"
+sequana-fastqc = "^1.5.0"
 pytest-cov = "^4.1.0"
 

sequana_pipetools/misc.py

@@ -87,26 +87,27 @@ def error(msg, pipeline):
 
 
 def print_version(name):
+
+    try:
+        ver = pkg_resources.require("sequana_{}".format(name))[0].version
+        print("sequana_{} version: {}".format(name, ver))
+    except Exception as err:
+        print(err)
+        print("sequana_{} version: ?".format(name))
+
     try:
         version = pkg_resources.require("sequana")[0].version
-        print("Sequana version used: {}".format(version))
+        print("Sequana version: {}".format(version))
     except Exception:  # pragma: no cover
         pass
 
     try:
         version = pkg_resources.require("sequana_pipetools")[0].version
-        print("Sequana_pipetools version used: {}".format(version))
+        print("Sequana_pipetools version: {}".format(version))
     except Exception as err:  # pragma: no cover
         print(err)
-        print("Sequana_pipetools version used: ?")
+        print("Sequana_pipetools version: ?")
 
-    try:
-        ver = pkg_resources.require("sequana_{}".format(name))[0].version
-        print("pipeline sequana_{} version used: {}".format(name, ver))
-    except Exception as err:
-        print(err)
-        print("pipeline sequana_{} version used: ?".format(name))
-        sys.exit(1)
     print(Colors().purple("\nHow to help ?\n- Please, consider citing us (see sequana.readthedocs.io)"))
     print(Colors().purple("- Contribute to the code or documentation"))
     print(Colors().purple("- Fill issues on https://github.com/sequana/sequana/issues/new/choose"))