Make code checks pass by diegoceccarelli · Pull Request #72 · AmenRa/ranx

diegoceccarelli · 2025-06-14T17:19:00Z

Fix linting issues and typos across the codebase

Description

This PR addresses various linting issues and typos identified by the linters (ruff, black, blackdoc, and typos). The changes include:

Removing >>> prompts from code blocks in markdown files
Fixing docstring examples in Python files
Correcting typos (e.g., "relevants" to "relevant")
Updating the ruff configuration to use the newer format
Replacing abbreviated journal name with full name in bibliographic references

Changes

Configuration

Updated pyproject.toml to use the newer ruff configuration format
Removed unused typos configuration

Documentation

Fixed code blocks in README.md and docs/index.md by removing >>> prompts
Updated journal name from Comput. Medical Imaging Graph. to Computerized Medical Imaging and Graphics in:
- ranx/fusion/isr.py
- ranx/fusion/logn_isr.py
- ranx/fusion/log_isr.py
- docs/fusion.md

Code

Fixed docstring examples in ranx/data_structures/report.py
Corrected typo "relevants" to "relevant" in:
- changelog.md
- ranx/metrics/interpolated_precision_at_recall.py

Testing

Ran make lint to verify that all linting checks pass:
- isort
- black
- blackdoc
- ruff
- typos

AmenRa · 2025-06-25T07:06:31Z

Hi, Diego and thanks for your contribution.

I guess we need to exclude some part of the codebase (the docs, mostly) from automatic fixes.

I need you to revert several changes:

README.md
1. The format of qrels and run dicts in README.md was chosen to make the code block more compact. I would prefer to keep them this way even if they are not black-formatted.
2. I think removing the ">>>" from the code block in README.md will make them less readable. With them its clear what comes afterwords is the output of the previous function call. Without them its less clear to me. Maybe it's just because I am used to them. I may agree to convert ">>>" in # output:. However, we lose color coding as they will appear as comments.
3. I prefer to keep in-line comments at 185 and 186 as-is. It is more readable.
docs/fusion.md
1. I prefer to keep in-line comments at 13 and 14 as-is. It is more readable.
docs/index.md
1. Same as the first point for README.md
2. Same as the second point for README.md
3. Same as the third point for README.md
docs/qrels.md
1. I prefer to keep in-line comments at 36 and 37 as-is. It is more readable.
2. I prefer to keep lines 52-56 as-is. It is more readable.
3. Line 72. I guess there is a typo here, which is not fixed by the proposed change.
4. I prefer to keep lines 86-89 as-is. It is more readable.
docs/run.md
1. I prefer to keep in-line comments at 37-39 as-is. It is more readable.
2. I prefer to keep lines 50-54 as-is. It is more readable.
3. Line 72. I guess there is a typo here, which is not fixed by the proposed change.
4. I prefer to keep lines 87-91 as-is. It is more readable.
ranx/data_structures/report.py
1. Not sure about the changes from 258 to 288.
ranx/metrics/interpolated_precision_at_recall.py
1. Why changing "relevants" to "relevant"? I guess this was an automatic change. Relavants is the short for "relevant documents".

AmenRa · 2025-06-25T10:04:54Z

docs/fusion.md

                    Jo{\~{a}}o Magalh{\~{a}}es},
        title     = {Multimodal medical information retrieval with unsupervised rank fusion},
-        journal   = {Comput. Medical Imaging Graph.},
+        journal   = {Computerized Medical Imaging and Graphics},


AmenRa · 2025-06-25T10:05:08Z

docs/fusion.md

                    Jo{\~{a}}o Magalh{\~{a}}es},
        title     = {Multimodal medical information retrieval with unsupervised rank fusion},
-        journal   = {Comput. Medical Imaging Graph.},
+        journal   = {Computerized Medical Imaging and Graphics},


AmenRa · 2025-06-25T10:05:17Z

docs/fusion.md

                    Jo{\~{a}}o Magalh{\~{a}}es},
        title     = {Multimodal medical information retrieval with unsupervised rank fusion},
-        journal   = {Comput. Medical Imaging Graph.},
+        journal   = {Computerized Medical Imaging and Graphics},


AmenRa · 2025-06-25T10:05:38Z

notebooks/2_qrels_and_run.ipynb

    "\n",
    "with open(\"notebooks/data/small_qrels.json\", \"w\") as f:\n",
-    "    master = f\"https://raw.githubusercontent.com/AmenRa/ranx/master/notebooks/data/small_qrels.json\"\n",
+    "    master = \"https://raw.githubusercontent.com/AmenRa/ranx/master/notebooks/data/small_qrels.json\"\n",


AmenRa · 2025-06-25T10:05:46Z

notebooks/2_qrels_and_run.ipynb

    "\n",
    "with open(\"notebooks/data/small_qrels.trec\", \"w\") as f:\n",
-    "    master = f\"https://raw.githubusercontent.com/AmenRa/ranx/master/notebooks/data/small_qrels.trec\"\n",
+    "    master = \"https://raw.githubusercontent.com/AmenRa/ranx/master/notebooks/data/small_qrels.trec\"\n",


AmenRa · 2025-06-25T10:06:00Z

ranx/fusion/isr.py

                        Jo{\~{a}}o Magalh{\~{a}}es},
            title     = {Multimodal medical information retrieval with unsupervised rank fusion},
-            journal   = {Comput. Medical Imaging Graph.},
+            journal   = {Computerized Medical Imaging and Graphics},


AmenRa · 2025-06-25T10:06:08Z

ranx/fusion/log_isr.py

                        Jo{\~{a}}o Magalh{\~{a}}es},
            title     = {Multimodal medical information retrieval with unsupervised rank fusion},
-            journal   = {Comput. Medical Imaging Graph.},
+            journal   = {Computerized Medical Imaging and Graphics},


AmenRa · 2025-06-25T10:06:17Z

ranx/fusion/logn_isr.py

                        Jo{\~{a}}o Magalh{\~{a}}es},
            title     = {Multimodal medical information retrieval with unsupervised rank fusion},
-            journal   = {Comput. Medical Imaging Graph.},
+            journal   = {Computerized Medical Imaging and Graphics},


AmenRa · 2025-06-25T10:06:34Z

ranx/meta/evaluate.py

AmenRa · 2025-06-25T10:07:20Z

I commented the changes to keep.

I think we should do the following.

Make `pyproject.toml` as follows:

[tool.ruff.lint]
# E501 ignore long comment lines (black should take care of that)
# E712 ignore == False, needed for numba checks.
ignore = ["E501", "E712"]

[tool.isort]
profile = "black"

Make `_typos.toml` as follows to ignore "relevants":

[default]
extend-ignore-identifiers-re = [
    ".*Hsi",
]

[default.extend-words]
# Prevent Typos from flagging these as typos
relevants = "relevants"

Remove `$(VENV_BIN)/blackdoc .` from `Makefile lint`.

Docs formatting is fine as-is, in my opinion.

- Fix tool configuration issues to prevent markdown formatting conflicts - Configure Black to exclude markdown files via pyproject.toml - Add IR-specific terminology ("relevants", "Comput") to typos ignore list - Fix syntax error in report.py docstring by changing code block type - Preserve reviewer-preferred formatting in documentation - Maintain all technical improvements while respecting human formatting preferences 🤖 Generated with [Claude Code](https://claude.ai/code) Co-Authored-By: Claude <noreply@anthropic.com>

diegoceccarelli · 2025-06-28T21:15:01Z

PR Updated - Reviewer Comments Addressed

I've updated this PR to address all the feedback. The branch has been rebased on master with a single clean commit.

Changes Made

🔧 Tool Configuration Fixes:

Configured Black to exclude markdown files via pyproject.toml to prevent formatting conflicts
Removed blackdoc from linting pipeline
Added IR-specific terminology to typos ignore list ("relevants", "Comput")

📝 Documentation Formatting Restored:

Reverted to reviewer-preferred compact dictionary formatting in README and docs
Restored aligned inline comments and >>> output patterns
Maintained IR domain terminology ("relevants" instead of "relevant")
Fixed syntax errors in documentation examples

🐛 Technical Fixes:

Fixed syntax error in report.py docstring by changing code block type from python to plain text
Preserved all technical improvements (bug fixes, type checking, tool updates)

Verification

The updated configuration ensures:

✅ make lint passes cleanly
✅ make fix-lint respects markdown file exclusions
✅ No formatting conflicts between tools and human preferences
✅ All technical improvements preserved

The linting pipeline is now streamlined to: isort → black → ruff → typos

diegoceccarelli · 2025-07-22T06:56:16Z

@AmenRa bump :)

diegoceccarelli requested a review from AmenRa June 19, 2025 06:38

diegoceccarelli mentioned this pull request Jun 25, 2025

docs: add docstring to Run.__init__ and fix type annotations #73

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AmenRa reviewed Jun 25, 2025

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ranx/meta/evaluate.py

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AmenRa Jun 25, 2025

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Ok.

diegoceccarelli force-pushed the fix-linting branch from 885c7eb to 75928d7 Compare June 28, 2025 21:11

AmenRa merged commit 914ff35 into master Jul 22, 2025
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diegoceccarelli commented Jun 14, 2025

Fix linting issues and typos across the codebase

Description

Changes

Configuration

Documentation

Code

Testing

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AmenRa commented Jun 25, 2025

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AmenRa commented Jun 25, 2025

Make pyproject.toml as follows:

Make _typos.toml as follows to ignore "relevants":

Remove $(VENV_BIN)/blackdoc . from Makefile lint.

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diegoceccarelli commented Jun 28, 2025 • edited Loading Uh oh! There was an error while loading. Please reload this page.

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PR Updated - Reviewer Comments Addressed

Changes Made

Verification

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diegoceccarelli commented Jul 22, 2025

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Make `pyproject.toml` as follows:

Make `_typos.toml` as follows to ignore "relevants":

Remove `$(VENV_BIN)/blackdoc .` from `Makefile lint`.

diegoceccarelli commented Jun 28, 2025 •

edited

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