[wip] reworking serialization #710
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WalkthroughThis update removes the Changes
Sequence Diagram(s)sequenceDiagram
participant Framework as Framework Script
participant Callee as callee.result()
participant Config as Config Namespace
participant File as Result File
Framework->>Callee: result(predictions, ... )
Callee->>Config: Access config.output_predictions_file
Callee->>Callee: Add "output_file" key to result dict if missing
Callee->>File: Dump result dict as JSON
Callee-->>Framework: Return result dict
sequenceDiagram
participant serialize_data
participant np as numpy
participant json as json_dump
serialize_data->>np: np.save(path, data, allow_pickle=False)
np-->>serialize_data: Success or ValueError (if object dtype)
alt object dtype array
serialize_data->>serialize_data: squeeze array
serialize_data->>json: json_dump(data.tolist(), path)
else non-object dtype array
serialize_data->>np: np.save(path, data, allow_pickle=False)
end
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Codecov ReportAttention: Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## master #710 +/- ##
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- Coverage 69.46% 51.10% -18.36%
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Files 57 36 -21
Lines 6821 5262 -1559
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- Hits 4738 2689 -2049
- Misses 2083 2573 +490 ☔ View full report in Codecov by Sentry. 🚀 New features to boost your workflow:
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Actionable comments posted: 2
🔭 Outside diff range comments (1)
amlb/utils/serialization.py (1)
219-235:⚠️ Potential issueReference to removed
config.numpy_picklebreaks.npzloading
numpy_allow_picklewas removed, yetdeserialize_data()still uses it:with np.load(path, allow_pickle=config.numpy_pickle) as loaded:This raises
AttributeError.
Given the new policy (“no pickle”), simply drop the arg:-with np.load(path, allow_pickle=config.numpy_pickle) as loaded: - return loaded +with np.load(path, allow_pickle=False) as loaded: + return loadedOptionally expose an explicit
allow_pickleflag inser_configif future flexibility is required.🧰 Tools
🪛 Pylint (3.3.7)
[refactor] 219-269: Unnecessary "elif" after "return", remove the leading "el" from "elif"
(R1705)
[refactor] 225-234: Unnecessary "else" after "return", remove the "else" and de-indent the code inside it
(R1705)
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📒 Files selected for processing (22)
amlb/utils/serialization.py(3 hunks)examples/custom/extensions/GradientBoosting/exec.py(0 hunks)examples/custom/extensions/Stacking/exec.py(0 hunks)frameworks/AutoGluon/exec.py(0 hunks)frameworks/AutoGluon/exec_ts.py(0 hunks)frameworks/FEDOT/exec.py(0 hunks)frameworks/FEDOT/exec_ts.py(0 hunks)frameworks/GAMA/exec.py(0 hunks)frameworks/H2OAutoML/exec.py(0 hunks)frameworks/MLPlan/exec.py(0 hunks)frameworks/NaiveAutoML/exec.py(0 hunks)frameworks/RandomForest/exec.py(0 hunks)frameworks/SapientML/exec.py(0 hunks)frameworks/TPOT/exec.py(0 hunks)frameworks/TunedRandomForest/exec.py(0 hunks)frameworks/autosklearn/exec.py(0 hunks)frameworks/flaml/exec.py(0 hunks)frameworks/hyperoptsklearn/exec.py(0 hunks)frameworks/lightautoml/exec.py(0 hunks)frameworks/mljarsupervised/exec.py(0 hunks)frameworks/oboe/exec.py(0 hunks)frameworks/shared/callee.py(1 hunks)
💤 Files with no reviewable changes (20)
- examples/custom/extensions/Stacking/exec.py
- frameworks/GAMA/exec.py
- frameworks/lightautoml/exec.py
- frameworks/oboe/exec.py
- frameworks/RandomForest/exec.py
- frameworks/mljarsupervised/exec.py
- frameworks/TunedRandomForest/exec.py
- frameworks/SapientML/exec.py
- frameworks/MLPlan/exec.py
- frameworks/TPOT/exec.py
- frameworks/hyperoptsklearn/exec.py
- frameworks/autosklearn/exec.py
- frameworks/flaml/exec.py
- frameworks/FEDOT/exec_ts.py
- frameworks/AutoGluon/exec_ts.py
- frameworks/H2OAutoML/exec.py
- frameworks/AutoGluon/exec.py
- examples/custom/extensions/GradientBoosting/exec.py
- frameworks/NaiveAutoML/exec.py
- frameworks/FEDOT/exec.py
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Actionable comments posted: 0
🧹 Nitpick comments (1)
.github/workflows/run_all_frameworks.yml (1)
167-172: Remove temporary "Check Things" debug step.This step listing venv directories is useful only during troubleshooting and clutters CI logs. Consider removing it or gating it behind a
debugflag once venv setup issues are resolved.
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Actionable comments posted: 1
🧹 Nitpick comments (1)
.github/workflows/run_all_frameworks.yml (1)
167-173: Eliminate Uselessechoand Quote Command Substitution
In the diagnostic step,echo $(pwd)is redundant—pwdalone suffices—and the unquoted command substitution could trigger word splitting. Replace:echo $(pwd)with:
pwdThis removes the unnecessary
echoand avoids potential splitting issues.🧰 Tools
🪛 actionlint (1.7.7)
168-168: shellcheck reported issue in this script: SC2046:warning:4:6: Quote this to prevent word splitting
(shellcheck)
168-168: shellcheck reported issue in this script: SC2005:style:4:6: Useless echo? Instead of 'echo $(cmd)', just use 'cmd'
(shellcheck)
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.github/workflows/run_all_frameworks.yml(1 hunks)frameworks/shared/setup.sh(1 hunks)
🧰 Additional context used
🪛 actionlint (1.7.7)
.github/workflows/run_all_frameworks.yml
168-168: shellcheck reported issue in this script: SC2046:warning:4:6: Quote this to prevent word splitting
(shellcheck)
168-168: shellcheck reported issue in this script: SC2005:style:4:6: Useless echo? Instead of 'echo $(cmd)', just use 'cmd'
(shellcheck)
⏰ Context from checks skipped due to timeout of 90000ms (3)
- GitHub Check: randomforest/kc2
- GitHub Check: randomforest/cholesterol
- GitHub Check: randomforest/iris
frameworks/shared/setup.sh
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| REQ_FILE="$SHARED_DIR/requirements.txt" | ||
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| for line in $(grep -vE '^\s*#' "$REQ_FILE" | grep -vE '^\s*$'); do | ||
| pkg=$(echo "$line" | sed -E 's/[=><~!].*$//') | ||
| # In a line like "numpy==1.12.0" then pkg=numpy and line is the whole line | ||
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| if ! PY -c "import $pkg" &> /dev/null; then | ||
| echo "$pkg not found. Installing from requirements.txt..." | ||
| PIP install --no-cache-dir "$line" | ||
| else | ||
| echo "$pkg is already installed by the framework, using that instead." | ||
| fi | ||
| done |
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🛠️ Refactor suggestion
Avoid word-splitting in the requirements loop
The for line in $(grep ...) construct will split on whitespace and may mis-handle requirements with spaces or special characters. Switch to a while IFS= read -r line pattern to preserve each line intact and eliminate the extra subshell:
- for line in $(grep -vE '^\s*#' "$REQ_FILE" | grep -vE '^\s*$'); do
+ while IFS= read -r line; do
pkg=${line%%[=><~!]*}
if ! PY -c "import $pkg" &> /dev/null; then
echo "$pkg not found. Installing from requirements.txt..."
PIP install --no-cache-dir "$line"
else
echo "$pkg is already installed by the framework, using that instead."
fi
- done
+ done < "$REQ_FILE"This approach avoids splitting issues, reduces forking (sed can be replaced with parameter expansion), and is more robust.
Committable suggestion skipped: line range outside the PR's diff.
🤖 Prompt for AI Agents
In frameworks/shared/setup.sh around lines 50 to 62, the loop uses `for line in
$(grep ...)` which causes word-splitting and can mishandle requirements with
spaces or special characters. Replace this loop with a `while IFS= read -r line`
construct to read each line intact without splitting. Also, remove the external
`sed` command by using shell parameter expansion to extract the package name
from each line. This will make the script more robust and efficient.
Ideal scenario there are only two formats left in the end:
but might need to support sparse data through scipy.
In any case I hope to avoid situations where pickle is used which leaks dependencies between libraries used by the benchmark software and the integration scripts.
Summary by CodeRabbit
Refactor
Chores
Tests
CI