Update dependencies to latest versions

Signed-off-by: Marcel Bargull <[email protected]>
bioconda · Mar 27, 2024 · ab8a293 · ab8a293
1 parent eda64b5
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diff --git a/bioconda_utils/bioconda_utils-requirements.txt b/bioconda_utils/bioconda_utils-requirements.txt
@@ -2,60 +2,70 @@
 # in ../docs/source/user/versions.rst
 # so please keep that documentation up to date as they change
 
-# basics
-python>=3.7
-conda=23.3.*
-boa=0.15.*
-conda-build=3.24.*
-conda-verify=3.1.*
-argh=0.26.*          # CLI
-colorlog=4.8.*       # Logging
-tqdm>=4.26           # Progress monitor
-yaspin =2
-ruamel_yaml=0.15.*   # Recipe YAML parsing
-pyaml=17.12.*        # Faster YAML parser (deprecate?)
-networkx=2.*
-pandas=1.4.*
-numpy=1.19.*         # Avoid breaking pandas on OSX
-libblas=*=*openblas  # Avoid large mkl package (pulled in by pandas)
-boltons=23.*
-jsonschema=3.2.*     # JSON schema verification
-pyopenssl>=22.1      # Stay compatible with cryptography
-
 # pinnings
 conda-forge-pinning=2023.05.06.13.08.41
 
-# tools
-anaconda-client=1.12.*  # anaconda_upload
-involucro=1.1.*        # mulled test and container build
-skopeo=1.11.*          # docker upload
-git=2.*                # well - git
+# basics
+python=3.11.*                 #
+conda=24.3.*                  #
+conda-libmamba-solver=24.1.*  #
+conda-build=24.3.*            #
+boa=0.17.*                    #
+
+argh=0.31.*                   # CLI
+colorlog=6.*                  # Logging
+tqdm=4.66.*                   # Progress monitor
+yaspin=2.*                    #
+ruamel.yaml=0.18.*            # Recipe YAML parsing
+pyaml=23.12.*                 # Faster YAML parser (deprecate?)
+networkx=3.2.*                #
+pandas=2.2.*                  #
+libblas=*=*openblas           # Avoid large mkl package (pulled in by pandas)
+boltons=23.*                  #
+jsonschema=4.21.*             # JSON schema verification
+jinja2=3.1.*                  #
+
+anaconda-client=1.12.*        # anaconda_upload
+galaxy-tool-util=23.*         # mulled test and container build
+involucro=1.1.*               # mulled test and container build
+skopeo=1.15.*                 # docker upload
+git=2.*                       # well - git
 
 # hosters - special regex not supported by RE
-regex=2022.7.9
+regex=2023.*                  #
 
 # asyncio
-aiohttp=3.8.*      # HTTP lib
-aiohttp-jinja2     # jinja2 renderer for aiohttp.web
-aiohttp-session
-aiohttp-security
-aiofiles=0.8.*     # async open
-aioftp=0.12.*      # FTP lib
-backoff=2.2.*      # retrying of failed API calls
-cachetools=3.0.*   # request caching (NEEDED?)
+aiohttp=3.9.*                 # HTTP lib
+aiohttp-jinja2                # jinja2 renderer for aiohttp.web
+aiohttp-session               #
+aiohttp-security              #
+aiofiles=23.*                 # async open
+aioftp=0.22.*                 # FTP lib
+backoff=2.2.*                 # retrying of failed API calls
+cachetools=5.3.*              # request caching (NEEDED?)
 
 # client API wrappers
-gitpython>=3.0.8,3.0.*    # githandler
-                          # needs >=3.0.8 due to https://github.com/conda-forge/staged-recipes/issues/10874
-gidgethub=3.0.*           # githubhandler
-pyjwt>=2.4.0              # githubhandler (JWT signing), needs >=2.4.0, CVE-2022-29217
+gitpython=3.1.*               # githandler
+gidgethub=5.*                 # githubhandler
+pyjwt>=2.4.0                  # githubhandler (JWT signing), needs >=2.4.0, CVE-2022-29217
+
+# bioconductor-skeleton
+beautifulsoup4=4.*            #
 
-# unknown
-beautifulsoup4=4.12.*
-galaxy-lib>=18.9.1
-jinja2>=2.10.1,<3
-markupsafe<2.1           # markupsafe 2.1 breaks jinja2
+# The bioconductor skeleton needs this
+requests=2.31.*               #
+
+# merge handling
+pygithub                      #
+
+# caching
+diskcache=5.*                 #
+platformdirs=4.*              #
 
+# build failure output
+tabulate=0.9.*                #
+
+# TODO: Remove these from general requirements into a doc-only-requirements file.
 # docs
 sphinx>=4.1
 celery
@@ -64,16 +74,3 @@ alabaster=0.7.*
 docutils
 markdown
 graphviz
-
-# The bioconductor skeleton needs this
-requests=2.29.*
-
-# merge handling
-pygithub
-
-# caching
-diskcache =5.*
-appdirs =1.*
-
-# build failure output
-tabulate =0.9
diff --git a/bioconda_utils/cli.py b/bioconda_utils/cli.py
@@ -56,7 +56,7 @@ def decorator(func):
         @arg('--logfile', help="Write log to file")
         @arg('--logfile-level', help="Log level for log file")
         @arg('--log-command-max-lines', help="Limit lines emitted for commands executed")
-        @utils.wraps(func)
+        @utils.wraps(func, hide_wrapped=True)
         def wrapper(*args, loglevel=default_loglevel, logfile=None,
                     logfile_level=default_file_loglevel,
                     log_command_max_lines=None, **kwargs):
@@ -125,7 +125,7 @@ def decorator(func):
                                  for field in allow_missing_for or []]
         except ValueError:
             sys.exit(f"Function {func} must have 'recipe_folder' and 'config' args")
-        @arg('recipe_folder', nargs='?',
+        @arg('recipe-folder', nargs='?',
              help='Path to folder containing recipes (default: recipes/)')
         @arg('config', nargs='?',
              help='Path to Bioconda config (default: config.yml)')
@@ -760,7 +760,7 @@ def dependent(recipe_folder, config, restrict=False,
      is specified, then all packages in a given bioconductor release will be
      created/updated (--force is then implied).''')
 @recipe_folder_and_config()
-@arg('bioc_data_packages', nargs='?',
+@arg('bioc-data-packages', nargs='?',
      help='''Path to folder containing the recipe for the bioconductor-data-packages
      (default: recipes/bioconductor-data-packages)''')
 @arg('--versioned', action='store_true', help='''If specified, recipe will be
@@ -851,8 +851,6 @@ def clean_cran_skeleton(recipe, no_windows=False):
     cran_skeleton.clean_skeleton_files(recipe, no_windows=no_windows)
 
 
-@arg('recipe_folder', help='Path to recipes directory')
-@arg('config', help='Path to yaml file specifying the configuration')
 @recipe_folder_and_config()
 @arg('--packages', nargs="+",
      help='Glob(s) for package[s] to scan. Can be specified more than once')

diff --git a/bioconda_utils/utils.py b/bioconda_utils/utils.py
@@ -34,7 +34,7 @@
 from yaspin import yaspin, Spinner
 from yaspin.spinners import Spinners
 from urllib3 import Retry
-import appdirs
+import platformdirs
 import diskcache
 
 from github import Github
@@ -66,7 +66,7 @@
 
 logger = logging.getLogger(__name__)
 
-disk_cache = diskcache.Cache(appdirs.user_cache_dir("bioconda-utils"))
+disk_cache = diskcache.Cache(platformdirs.user_cache_dir("bioconda-utils"))
 
 
 class TqdmHandler(logging.StreamHandler):
@@ -120,7 +120,7 @@ def ensure_list(obj):
     return [obj]
 
 
-def wraps(func):
+def wraps(func, hide_wrapped=False):
     """Custom wraps() function for decorators
 
     This one differs from functiools.wraps and boltons.funcutils.wraps in
@@ -151,6 +151,10 @@ def wrapper_wrapper(wrapper_func):
         fully_wrapped.__wrapped__ = func
         return fully_wrapped
 
+    if hide_wrapped and hasattr(fully_wrapped, '__wrapped__'):
+        del fully_wrapped.__dict__['__wrapped__']
+    elif not hide_wrapped:
+        fully_wrapped.__wrapped__ = func
     return wrapper_wrapper