Migrate to Miniforge #22
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Outside diff range, codebase verification and nitpick comments (1)
tests/basemap_example.py (1)
17-22: Avoid using semicolons.The data generation is correctly implemented, but the use of semicolons can be avoided for better readability.
Apply this diff to avoid using semicolons:
-nlats = 73; nlons = 145; delta = 2.*np.pi/(nlons-1) +lats = 73 +nlons = 145 +delta = 2.*np.pi/(nlons-1)Tools
Ruff
18-18: Multiple statements on one line (semicolon)
(E702)
18-18: Multiple statements on one line (semicolon)
(E702)
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- CHANGELOG.md (1 hunks)
- Miniforge3/.gitignore (1 hunks)
- install_miniforge.bash (21 hunks)
- tests/basemap_example.py (1 hunks)
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tests/basemap_example.py
18-18: Multiple statements on one line (semicolon)
(E702)
18-18: Multiple statements on one line (semicolon)
(E702)
LanguageTool
CHANGELOG.md
[style] ~18-~18: Consider using a different verb for a more formal wording.
Context: ... Make a symlink off2pytof2py3to fix an issue with the wrongf2pybeing fo...(FIX_RESOLVE)
Shellcheck
install_miniforge.bash
[warning] 435-435: Use "$@" (with quotes) to prevent whitespace problems.
(SC2048)
[warning] 658-658: Use "${var:?}" to ensure this never expands to / .
(SC2115)
Additional comments not posted (12)
tests/basemap_example.py (4)
1-3: LGTM!The import statements are necessary and correctly implemented.
The code changes are approved.
4-16: LGTM!The map setup and drawing are correctly implemented.
The code changes are approved.
23-27: LGTM!The computation of map projection coordinates and contouring data is correctly implemented.
The code changes are approved.
28-28: LGTM!The plot display is correctly implemented.
The code changes are approved.
CHANGELOG.md (3)
14-17: LGTM!The documentation of the migration to Miniforge is clear and correctly reflects the changes.
The code changes are approved.
22-27: LGTM!The documentation of the added packages is clear and correctly reflects the changes.
The code changes are approved.
31-35: LGTM!The documentation of the removed packages and options is clear and correctly reflects the changes.
The code changes are approved.
install_miniforge.bash (5)
6-15: LGTM!The logic for saving and restoring
.mambarcis correctly implemented.The code changes are approved.
Also applies to: 18-29
62-94: LGTM!The usage function is correctly updated to reflect Miniforge.
The code changes are approved.
151-164: LGTM!The command line arguments are correctly updated to reflect Miniforge.
The code changes are approved.
Line range hint
303-318: LGTM!The Miniforge version variables are correctly set.
The code changes are approved.
Line range hint
439-451: LGTM!The package installation logic is correctly implemented.
The code changes are approved.
Also applies to: 466-573, 611-625
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Outside diff range, codebase verification and nitpick comments (1)
CHANGELOG.md (1)
31-35: Inconsistency Found:--condaOption Still Present in DocumentationThe
--condaoption is still mentioned in theREADME.mdfile, despite its removal being noted in theCHANGELOG.md. Please ensure that the documentation is updated to accurately reflect the current state of the codebase.
README.md: Mentions--condaoption.CHANGELOG.md: States removal of--condaoption.Analysis chain
Confirm removal of packages and options.
The removal of the
--condaoption and packages likeredis-pyandsphinxcontribdue to their unavailability is noted. Ensure that these packages are indeed not needed or replaced by alternatives in the project.Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Verify the removal of `redis-py` and `sphinxcontrib` packages grep -r 'redis-py\|sphinxcontrib' .Length of output: 277
Script:
#!/bin/bash # Verify the removal of the `--conda` option grep -r '--conda' .Length of output: 138
Script:
#!/bin/bash # Corrected command to verify the removal of the `--conda` option grep -r '\-\-conda' .Length of output: 405
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- Miniforge3/.gitignore (1 hunks)
- install_miniforge.bash (21 hunks)
- tests/basemap_example.py (1 hunks)
Files skipped from review due to trivial changes (1)
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Files skipped from review as they are similar to previous changes (2)
- .gitignore
- tests/basemap_example.py
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CHANGELOG.md
[style] ~18-~18: Consider using a different verb for a more formal wording.
Context: ... Make a symlink off2pytof2py3to fix an issue with the wrongf2pybeing fo...(FIX_RESOLVE)
Shellcheck
install_miniforge.bash
[warning] 435-435: Use "$@" (with quotes) to prevent whitespace problems.
(SC2048)
[warning] 658-658: Use "${var:?}" to ensure this never expands to / .
(SC2115)
Additional comments not posted (8)
CHANGELOG.md (2)
14-17: Document migration to Miniforge clearly.The explanation regarding the versioning of Miniforge compared to Miniconda is clear and helps prevent misunderstandings about the version change.
22-27: Review package management changes.The switch to "Explicit Mamba Packages" and the movement of
redisfrom Mamba to Pip are well-documented. These changes align with the PR's objectives to streamline package management.install_miniforge.bash (6)
6-15: Proper handling of user's .mambarc file.The script correctly checks for an existing
.mambarcfile and backs it up before proceeding. This is a good practice to avoid losing user configurations.
18-27: Ensure cleanup function restores configurations.The cleanup function is designed to restore the original
.mambarcfile if it was modified. This is crucial for not disrupting user settings after the script execution.
62-94: Review updated usage instructions.The usage instructions have been updated to reflect the transition to Miniforge. The examples and descriptions are clear, making it easy for users to understand how to use the script.
Line range hint
151-200: Check parameter handling in script.The script handles command-line arguments for Miniforge version and installation directory. Ensure that these parameters are correctly parsed and used in the script.
Line range hint
303-550: Validate new Miniforge installation logic.The script sets up Miniforge-specific variables and handles the installation process. The use of
mambafor package installation is noted, aligning with the migration to Miniforge.
Line range hint
611-625: Inspect Pip package installations.The script installs several packages using Pip, including
redis, which has been moved from Mamba to Pip as per the PR objectives. This change should be verified to ensure it aligns with project requirements.Verification successful
Redis is installed using Pip as intended.
The
redispackage is being installed using thePIP_INSTALLvariable in theinstall_miniforge.bashscript. This aligns with the PR objectives of movingredisinstallation from Mamba to Pip.
- The installation command is found in
install_miniforge.bash.Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Verify the installation of `redis` and other critical packages grep -r 'pip install redis' .Length of output: 31
Script:
#!/bin/bash # Search for the usage of the PIP_INSTALL variable and any pip installations of redis grep -r 'PIP_INSTALL.*redis' .Length of output: 76
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CHANGELOG.md
[style] ~18-~18: Consider using a different verb for a more formal wording.
Context: ... Make a symlink off2pytof2py3to fix an issue with the wrongf2pybeing fo...(FIX_RESOLVE)
Shellcheck
install_miniforge.bash
[warning] 461-461: Use "$@" (with quotes) to prevent whitespace problems.
(SC2048)
[warning] 679-679: Use "${var:?}" to ensure this never expands to / .
(SC2115)
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CHANGELOG.md (4)
14-17: LGTM!The migration from Miniconda to Miniforge is correctly documented.
19-20: LGTM!The update to
.condarcand.mambarcto use theconda-forgechannel is correctly documented.
24-29: LGTM!The changes to the package management, including explicit Mamba and Pip packages, are correctly documented.
33-38: LGTM!The removal of the
--condaoption and defunct packages is correctly documented.install_miniforge.bash (6)
6-16: LGTM!The logic for saving and restoring
.mambarcand.condarcis correct.Also applies to: 27-37
76-111: LGTM!The usage instructions are correctly updated to reflect Miniforge.
Line range hint
167-216: LGTM!The command line arguments are correctly updated to reflect Miniforge.
Line range hint
319-334: LGTM!The version variables are correctly updated to reflect Miniforge.
Line range hint
337-352: LGTM!The architecture detection is correctly updated to reflect Miniforge.
Line range hint
360-742: LGTM!The installation steps are correctly updated to reflect Miniforge.
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Outside diff range, codebase verification and nitpick comments (1)
README.md (1)
16-16: Specify a language for the fenced code block.Specifying a language for the fenced code block improves readability and syntax highlighting.
Apply this diff to specify the language for the fenced code block:
-``` +```bashTools
Markdownlint
16-16: null
Fenced code blocks should have a language specified(MD040, fenced-code-language)
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- tests/numpy_example.py (1 hunks)
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README.md
[style] ~13-~13: Consider a shorter alternative to avoid wordiness.
Context: ...ith an error message. ## Installation In order to use the install script, you can run: `...(IN_ORDER_TO_PREMIUM)
[grammar] ~14-~14: The word ‘install’ is not a noun.
Context: .... ## Installation In order to use the install script, you can run: ``` ./install_min...(A_INSTALL)
Markdownlint
README.md
16-16: null
Fenced code blocks should have a language specified(MD040, fenced-code-language)
Shellcheck
install_miniforge.bash
[warning] 461-461: Use "$@" (with quotes) to prevent whitespace problems.
(SC2048)
[warning] 679-679: Use "${var:?}" to ensure this never expands to / .
(SC2115)
Additional comments not posted (19)
tests/numpy_example.py (4)
50-50: LGTM!The reduction in size for
vector_mulfrom 8192 to 1024 likely optimizes performance or resource usage.
51-51: LGTM!The reduction in size for
matrix_mulfrom 8192 to 1024 likely optimizes performance or resource usage.
52-52: LGTM!The reduction in size for
svd_decompositionfrom 2048 to 512 likely optimizes performance or resource usage.
53-53: LGTM!The reduction in size for
eigen_decompositionfrom 2048 to 512 likely optimizes performance or resource usage.README.md (5)
8-10: LGTM!The change to use Miniforge and restrict the installation to
conda-forgeandnodefaultsenhances control over package sources and prevents potential conflicts with the Anacondadefaultschannel.
17-17: LGTM!The update to use
install_miniforge.bashinstead ofinstall_miniconda.bashreflects the transition from Miniconda to Miniforge.
31-35: LGTM!The update to the usage instructions ensures that they are accurate and up-to-date with the changes in the installation script.
49-49: LGTM!The update provides clarity on how the installation path is determined based on the Miniforge version, Python version, and the date of the installation.
58-62: LGTM!The update ensures that the installation uses
conda-forgeas the default channel by creating or substituting a.mambarcand.condarcfile in the user's home directory.install_miniforge.bash (10)
6-16: LGTM!The update ensures that the user's original
.mambarcand.condarcconfiguration files are preserved.
27-37: LGTM!The update ensures that the user's original
.mambarcand.condarcconfiguration files are restored after the script execution.
80-111: LGTM!The update to the usage instructions ensures that they are accurate and up-to-date with the changes in the installation script.
Line range hint
319-334: LGTM!The update to the Miniforge version variables reflects the transition from Miniconda to Miniforge.
Line range hint
337-352: LGTM!The update to the Miniforge architecture settings reflects the transition from Miniconda to Miniforge.
360-362: LGTM!The update ensures that the installation directory is created if it does not exist.
366-367: LGTM!The update to the Miniforge installation directory settings reflects the transition from Miniconda to Miniforge.
442-442: LGTM!The update to the Miniforge environment creation settings reflects the transition from Miniconda to Miniforge.
491-491: LGTM!The update to the mamba package installation settings reflects the transition from Miniconda to Miniforge.
Line range hint
632-646: LGTM!The update to the pip package installation settings reflects the transition from Miniconda to Miniforge.
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Outside diff range, codebase verification and nitpick comments (1)
install_miniforge.bash (1)
Line range hint
212-752: LGTM!The code changes comprehensively migrate the installation process from Miniconda to Miniforge. The variable names, file paths, and URLs have been updated consistently, and the package installation commands have been modified appropriately.
Address Shellcheck warnings.
Shellcheck has raised the following warnings:
- Line 466: Use
"$@"(with quotes) to prevent whitespace problems.- Line 689: Use
"${var:?}"to ensure this never expands to/.To address these warnings, apply the following changes:
- Line 466: Change
$*to"$@".- $MAMBA_INSTALL_COMMAND $* + $MAMBA_INSTALL_COMMAND "$@"
- Line 689: Change
$MINIFORGE_SRCDIRto"${MINIFORGE_SRCDIR:?}".- rm -rf $MINIFORGE_SRCDIR/$PYGRADS_VERSION + rm -rf "${MINIFORGE_SRCDIR:?}/$PYGRADS_VERSION"
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CHANGELOG.md
[style] ~18-~18: Consider using a different verb for a more formal wording.
Context: ... Make a symlink off2pytof2py3to fix an issue with the wrongf2pybeing fo...(FIX_RESOLVE)
Shellcheck
install_miniforge.bash
[warning] 466-466: Use "$@" (with quotes) to prevent whitespace problems.
(SC2048)
[warning] 689-689: Use "${var:?}" to ensure this never expands to / .
(SC2115)
Additional comments not posted (9)
CHANGELOG.md (5)
14-17: LGTM!The changes are approved.
19-22: LGTM!The changes are approved.
26-31: LGTM!The changes are approved.
35-41: LGTM!The changes are approved.
18-18: Skipping the style suggestion.The current wording is acceptable in a changelog.
Tools
LanguageTool
[style] ~18-~18: Consider using a different verb for a more formal wording.
Context: ... Make a symlink off2pytof2py3to fix an issue with the wrongf2pybeing fo...(FIX_RESOLVE)
install_miniforge.bash (4)
6-16: LGTM!The code changes are approved. Safely backing up the user's existing
.mambarcfile is a good practice.
27-37: LGTM!The code changes are approved. The cleanup function correctly restores the user's original
.mambarcand.condarcfiles.
76-91: LGTM!The code changes are approved. The usage function has been updated to accurately reflect the Miniforge migration.
Line range hint
160-183: LGTM!The code changes are approved. The new
--ffnet-hackcommand line argument and the correspondingFFNET_HACKvariable are correctly implemented.
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CHANGELOG.md
[style] ~28-~28: Consider using a different verb for a more formal wording.
Context: ... Make a symlink off2pytof2py3to fix an issue with the wrongf2pybeing fo...(FIX_RESOLVE)
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CHANGELOG.md (2)
36-41: LGTM!The added packages and the basemap example are consistent with the list of alterations and align with the PR objectives.
45-50: Removed packages and options look good!The removed packages and options are consistent with the list of alterations and align with the PR objectives. The reasoning for each removal is clearly explained.
Due to Anaconda/Miniconda licensing concerns, this PR moves GEOSpyD to a pure Miniforge set up.
Beyond the scripting fixes to make this work, we also remove
redis-pyandsphinxcontribas packages as they seem to be defunct (not sure).We also move the
redispackage from a Mamba install to a Pip install.