Add pixi support #6157
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Add pixi support #6157
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- Introduced PixiConfig and PixiCache classes for managing Pixi environments. - Updated Session class to include PixiConfig retrieval. - Enhanced CmdRun with options to enable/disable Pixi environments. - Modified ConfigBuilder to apply Pixi environment settings based on command-line options. - Updated BashWrapperBuilder to include Pixi activation in the execution script. - Added pixiEnv property to TaskBean and methods in TaskRun for Pixi environment handling. - Updated ProcessConfig to include 'pixi' in process configuration options. This commit integrates Pixi environment management into the Nextflow framework, allowing users to specify and control Pixi environments during execution. Signed-off-by: Edmund Miller <[email protected]>
- Introduced PixiCacheTest and PixiConfigTest classes to validate Pixi environment functionality. - Added tests for TOML and lock file detection, environment prefix path creation, and command execution handling. - Implemented checks for configuration options and cache directory retrieval in PixiConfig. This commit enhances the test coverage for Pixi environment management, ensuring robust functionality within the Nextflow framework. Signed-off-by: Edmund Miller <[email protected]>
- Introduced PixiCacheIntegrationTest class to validate PixiCache behavior with various environment specifications. - Implemented tests for creating environments from package specifications, TOML files, and lock files. - Added checks for handling custom cache directories and validating TOML and lock file detection. - Enhanced coverage for existing prefix directory handling and environment variable cache directory usage. This commit strengthens the testing framework for PixiCache, ensuring reliable environment management within the Nextflow ecosystem. Signed-off-by: Edmund Miller <[email protected]>
- Changed the environment specification from 'python=3.8' to 'cowpy'. - Updated the script to utilize cowpy for output instead of a Python command. This modification enhances the testing of Pixi environments by leveraging cowpy for greeting functionality.
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| if( pixiFile.exists() ) { | ||
| // Read the project directory path | ||
| final projectDir = pixiFile.text.trim() | ||
| result += "cd ${Escape.path(projectDir as String)} && " | ||
| result += "eval \"\$(pixi shell-hook --shell bash)\" && " | ||
| result += "cd \"\$OLDPWD\"\n" | ||
| } | ||
| else { | ||
| // Direct activation from environment directory | ||
| result += "cd ${Escape.path(pixiEnv)} && " | ||
| result += "eval \"\$(pixi shell-hook --shell bash)\" && " | ||
| result += "cd \"\$OLDPWD\"\n" | ||
| } | ||
| return result |
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Where is OLDPWD defined? Doesn't this change to the projectDir? Should we overwrite projectDir with the pixiFile contents?
While it's uncessary duplication, I prefer copying the pixi lock file into the working dir and using it at source, so we have a record. This has the additional advantage of making the code more simple and supporting a .pixi or pixi.lock file (psuedocode):
Suggested change
| if( pixiFile.exists() ) { | |
| // Read the project directory path | |
| final projectDir = pixiFile.text.trim() | |
| result += "cd ${Escape.path(projectDir as String)} && " | |
| result += "eval \"\$(pixi shell-hook --shell bash)\" && " | |
| result += "cd \"\$OLDPWD\"\n" | |
| } | |
| else { | |
| // Direct activation from environment directory | |
| result += "cd ${Escape.path(pixiEnv)} && " | |
| result += "eval \"\$(pixi shell-hook --shell bash)\" && " | |
| result += "cd \"\$OLDPWD\"\n" | |
| } | |
| return result | |
| // assuming you have copied the pixi file to working dir | |
| if( pixiFile.exists() ) { | |
| result += "[ -d .pixi ] && [ -f pixi.lock ] || pixi install" | |
| result += "eval \"\$(pixi shell-hook --shell bash)\"" | |
| } | |
| return result |
Downside - massive duplication of text files in every work dir.
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