Merge pull request #1361 from opencobra/update-depinfo

Update depinfo

.github/ISSUE_TEMPLATE/01-bug-report.yaml

@@ -0,0 +1,64 @@
+name: 🐞 Bug report
+description: Report a problem to help improve this project
+title: "[BUG] "
+labels: [bug, triage]
+body:
+    - type: checkboxes
+      attributes:
+          label: Is there an existing issue for this?
+          description: Please search to see if an [issue already exists](https://github.com/opencobra/cobrapy/issues) for the bug you encountered.
+          options:
+              - label: I have searched the existing issues
+                required: true
+    - type: textarea
+      attributes:
+          label: Problem description
+          description: |
+              A concise description of what you're experiencing.
+
+              Please explain:
+
+                * **what** you tried to achieve,
+                * **how** you went about it (referring to the code sample), and
+                * **why** the current behaviour is a problem and what output you expected instead.
+      validations:
+          required: false
+    - type: textarea
+      attributes:
+          label: Code sample
+          description: >
+              Create a [minimal, complete, verifiable example](https://stackoverflow.com/help/mcve).
+              Please, paste your code between the ``` tickmarks below or link to a [gist](https://gist.github.com/).
+          value: |
+              Code run:
+
+              ```python
+              ```
+
+              Traceback:
+
+              ```text
+              ```
+      validations:
+          required: false
+    - type: textarea
+      attributes:
+          label: Environment
+          description: >
+              Please paste the output of running `depinfo --markdown cobra`
+              in your environment between the `details` tags below.
+          value: |
+              <details>
+
+              </details>
+      validations:
+          required: true
+    - type: textarea
+      attributes:
+          label: Anything else?
+          description: |
+              Links? References? Anything that will give us more context about the issue you are encountering!
+
+              Tip: You can attach images or log files by clicking this area to highlight it and then dragging files in.
+      validations:
+          required: false

.github/ISSUE_TEMPLATE/02-feature-request.yaml

@@ -0,0 +1,46 @@
+
+name: Feature request
+description: Suggest an idea for this project
+title: "[Feature] "
+labels: [enhancement]
+body:
+    - type: checkboxes
+      attributes:
+          label: Checklist
+          description: >
+              Please make sure you check all these items before submitting your feature request.
+          options:
+              - label: There are [no similar issues or pull requests](https://github.com/opencobra/cobrapy/issues) for this yet.
+                required: true
+    - type: textarea
+      attributes:
+          label: Problem
+          description: >
+              A clear and concise description of what you are trying to achieve.
+          placeholder: >
+              "I want to be able to [...] but I can't because [...]".
+      validations:
+          required: false
+    - type: textarea
+      attributes:
+          label: Solution
+          description: >
+              A clear and concise description of what you would want to happen.
+              For API changes, try to provide a code snippet of what you would like the new API to look like.
+      validations:
+          required: false
+    - type: textarea
+      attributes:
+          label: Alternatives
+          description: >
+              Please describe any alternative solutions or features you've considered to solve
+              your problem and why they didn't help.
+      validations:
+          required: false
+    - type: textarea
+      attributes:
+          label: Anything else?
+          description: >
+              Provide any additional context, screenshots, tracebacks, etc. about the feature here.
+      validations:
+          required: false

.github/ISSUE_TEMPLATE/config.yml

@@ -1,11 +1,10 @@
 # Ref: https://help.github.com/en/github/building-a-strong-community/configuring-issue-templates-for-your-repository#configuring-the-template-chooser
 blank_issues_enabled: true
 contact_links:
-- name: 📧 Google Group
-  url: http://groups.google.com/group/cobra-pie
+- name: Question
+  url: https://github.com/opencobra/cobrapy/discussions
   about: >
-    Please ask typical questions here: General constraint-based modelling problems or
-    issues with genome-scale models in COBRApy.
+    Please ask general questions about constraint-based modeling or COBRApy specifically here.
 - name: 💬 Gitter
   url: https://gitter.im/opencobra/cobrapy
   about: >

release-notes/next-release.md

@@ -6,6 +6,8 @@
 
 ## Other
 
+* Updated the package `depinfo` to version >2.
+
 ## Deprecated features
 
 ## Backwards incompatible changes

setup.cfg

@@ -6,7 +6,7 @@ parse = (?P<major>\d+)
 	\.(?P<minor>\d+)
 	\.(?P<patch>\d+)
 	(?P<release>[a]*)(?P<num>\d*)
-serialize = 
+serialize =
 	{major}.{minor}.{patch}{release}{num}
 	{major}.{minor}.{patch}
 tag_name = {new_version}
@@ -15,15 +15,15 @@ tag_name = {new_version}
 name = cobra
 url = https://opencobra.github.io/cobrapy
 download_url = https://pypi.org/project/cobra
-project_urls = 
+project_urls =
 	Source Code = https://github.com/opencobra/cobrapy
 	Documentation = https://cobrapy.readthedocs.io
 	Bug Tracker = https://github.com/opencobra/cobrapy/issues
 author = The cobrapy core development team.
 author_email = cobra-pie@googlegroups.com
 maintainer = Moritz E. Beber
 maintainer_email = moritz.beber@gmail.com
-classifiers = 
+classifiers =
 	Development Status :: 5 - Production/Stable
 	Intended Audience :: Science/Research
 	License :: OSI Approved :: GNU General Public License v2 or later (GPLv2+)
@@ -40,7 +40,7 @@ license = LGPL-2.0-or-later OR GPL-2.0-or-later
 description = COBRApy is a package for constraint-based modeling of metabolic networks.
 long_description = file: README.rst, INSTALL.rst
 long_description_content_type = text/x-rst
-keywords = 
+keywords =
 	metabolism
 	biology
 	constraint-based
@@ -52,9 +52,9 @@ keywords =
 
 [options]
 zip_safe = True
-install_requires = 
+install_requires =
 	appdirs ~=1.4
-	depinfo ~=1.7
+	depinfo ~=2.2
 	diskcache ~=5.0
 	future
 	httpx ~=0.24
@@ -67,24 +67,24 @@ install_requires =
 	rich >=8.0
 	ruamel.yaml ~=0.16
 	swiglpk
-tests_require = 
+tests_require =
 	tox
 packages = find:
-package_dir = 
+package_dir =
 	= src
 
 [options.packages.find]
 where = src
 
 [options.package_data]
-cobra = 
+cobra =
 	data/*
 	io/*.json
 
 [options.extras_require]
-array = 
+array =
 	scipy
-development = 
+development =
 	black
 	bumpversion
 	isort
@@ -96,7 +96,7 @@ universal = 1
 [bumpversion:part:release]
 optional_value = placeholder
 first_value = placeholder
-values = 
+values =
 	placeholder
 	a
 

src/cobra/util/util.py

@@ -3,7 +3,7 @@
 import textwrap
 from typing import Any
 
-from depinfo import print_dependencies
+from depinfo.application import DisplayApplication
 
 
 def format_long_string(string: str, max_length: int = 50) -> str:
@@ -59,4 +59,4 @@ def __getitem__(self, item: Any) -> Any:
 
 def show_versions() -> None:
     """Print dependency information."""
-    print_dependencies("cobra")
+    DisplayApplication.run("cobra")

tests/test_util/test_util.py

@@ -39,11 +39,9 @@ def test_show_versions(capsys) -> None:
     show_versions()
     captured = capsys.readouterr()
     lines = captured.out.split("\n")
-    assert lines[1].startswith("System Information")
-    assert lines[2].startswith("==================")
-    assert lines[3].startswith("OS")
-    assert lines[4].startswith("OS-release")
-    assert lines[5].startswith("Python")
-
-    assert lines[7].startswith("Package Versions")
-    assert lines[8].startswith("================")
+    assert lines[1].startswith("Package Information")
+    assert lines[2].startswith("------------------")
+    assert lines[3].startswith("cobra")
+
+    assert lines[5].startswith("Dependency Information")
+    assert lines[6].startswith("------------------")