Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Update meta.yaml #51670

Closed
wants to merge 12 commits into from
Closed

Update meta.yaml #51670

Changes from 11 commits
Commits
Show all changes
12 commits
Select commit Hold shift + click to select a range
53a804f
Update meta.yaml
KennthShang Oct 25, 2024
ae2648b
Update meta.yaml
KennthShang Oct 26, 2024
ed1cda7
Update meta.yaml
KennthShang Oct 26, 2024
63899c1
Update meta.yaml
KennthShang Oct 26, 2024
7d2945f
Update meta.yaml
KennthShang Oct 26, 2024
d7b9fde
Update meta.yaml
KennthShang Oct 26, 2024
dc796a5
Update meta.yaml
KennthShang Oct 26, 2024
1cf1c64
Update meta.yaml
KennthShang Oct 26, 2024
637c7e8
Merge branch 'master' into patch-1
KennthShang Oct 26, 2024
47691e5
Update meta.yaml
KennthShang Oct 26, 2024
e577c47
Update meta.yaml
KennthShang Oct 26, 2024
a145803
Update meta.yaml
KennthShang Oct 26, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
28 changes: 16 additions & 12 deletions recipes/phabox/meta.yaml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -10,7 +10,7 @@ source:
sha256: 0ffe4da03ccc2aac77c17866033ce513f72a5ecdf9df108abbcdbfced438b04c

build:
number: 0
number: 1
noarch: python
script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv"
entry_points:
Expand All @@ -20,25 +20,28 @@ build:

requirements:
host:
- pip
- python >=3.8
- setuptools
run:
- python >=3.8
- python >=3.10
Copy link
Contributor

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

⚠️ Potential issue

Fix Python version mismatch between host and run requirements.

The host section specifies python >=3.8 while the run section requires python >=3.10. This mismatch could cause build issues.

  host:
-   - python >=3.8
+   - python >=3.10

Committable suggestion was skipped due to low confidence.

- diamond =0.9.14
KennthShang marked this conversation as resolved.
Show resolved Hide resolved
- blast >=2.16.0
- mcl >=22.282
- prodigal-gv >=2.11.0
- biopython >=1.84
- datasets >=3
- datasets >=3.0.2
- kcounter >=0.1.1
- fasttree >=2.1.11
- mafft >=7.525
- networkx >=3.4
- networkx >=3.4.2
- numpy >=1.26
- pandas >=2
- prodigal-gv >=2.11.0
- pyarrow >=16
- pytorch >=2.4
- scipy >=1.14
- pandas >=2.2.3
- pyarrow >=16.1.0
- pytorch >=2.4.0
Copy link
Contributor

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

⚠️ Potential issue

Update package versions to available releases.

Several specified package versions are not currently available in conda-forge:

  • PyTorch 2.4.0 is not yet released
  • Some version constraints are too strict

Consider using these available versions:

-    - pytorch >=2.4.0
+    - pytorch >=2.1.0
-    - transformers >=4.11.3
-    - triton >=2.0.0
+    - transformers >=4.11.3,<5.0
+    - triton >=2.0.0,<3.0

Also applies to: 37-38

Copy link
Contributor

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

⚠️ Potential issue

PyTorch 2.4.0 is not yet released.

The specified PyTorch version 2.4.0 is a future version that hasn't been released yet. This will cause package installation failures.

Use the latest stable version instead:

- pytorch >=2.4.0
+ pytorch >=2.1.0
📝 Committable suggestion

‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.

Suggested change
- pytorch >=2.4.0
- pytorch >=2.1.0

- scipy >=1.14.1
- seaborn-base >=0.13.2
- transformers >=4
- transformers >=4.11.3
- triton >=2.0.0

test:
commands:
Expand All @@ -49,7 +52,7 @@ about:
license: "AFL-3.0"
license_family: OTHER
license_file: "LICENSE.md"
summary: "Phage BOX is a Python library for phage-related tasks."
summary: "PhaBOX is a Python library for virus-related tasks."
dev_url: "https://github.com/KennthShang/PhaBOX"
doc_url: "https://github.com/KennthShang/PhaBOX/wiki"

Expand All @@ -59,3 +62,4 @@ extra:
identifiers:
- doi:10.1093/bioadv/vbad101
- biotools:phabox