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| ## Changelog | ||
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| ### To-do | ||
| * Fix documentation issues [ ] | ||
| * Add subpackage docstrings [ ] | ||
| * Create methods for Sample and Project | ||
| * .describe [ ] | ||
| * .write_paths_to_file, .copy_files_to_dir(), .link_files_to_dir() [ ] | ||
| * .total_duration [ ] | ||
| * Add logger calls when saving to JSON and uploading to ProvStore [ ] | ||
| * [ ] Fix documentation issues | ||
| * [ ] Add subpackage docstrings | ||
| * [ ] Create methods for Sample and Pro | ||
| * [ ] .describe | ||
| * [ ] .write_paths_to_file, .copy_files_to_dir(), .link_files_to_dir() | ||
| * [ ] .total_duration | ||
| * [ ] Add logger calls when saving to JSON and uploading to ProvStore | ||
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| ### v0.1.24 | ||
| * State requirements more clearly [x] | ||
| * Improve error handling when getting `Program` attributes [x] | ||
| * Add `__doc__` variable to modules to build documentation [x] | ||
| * Fix `File.size` property [x] | ||
| * Add `File.raw_size` property [x] | ||
| * [x] State requirements more clearly | ||
| * [x] Improve error handling when getting `Program` attributes | ||
| * [x] Add `__doc__` variable to modules to build documentation | ||
| * [x] Fix `File.size` property | ||
| * [x] Add `File.raw_size` property | ||
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| ### v0.1.23 | ||
| * Patch PresetProgram SeqFile addition feature [x] | ||
| * Fix SeqFile deserializer [x] | ||
| * Add import_records arg to `bp.load_project()` [x] | ||
| * Improve reserved aminoacid characters [x] | ||
| * Add `SeqFile.max_seq` and `.min_seq` properties [x] | ||
| * Patch `Project` deserializer to improve BioProvDocument creation [x] | ||
| * Make shorter Environment hashes [x] | ||
| * Improve Project `__repr__` [x] | ||
| * [x] Patch PresetProgram SeqFile addition feature | ||
| * [x] Fix SeqFile deserializer | ||
| * [x] Add import_records arg to `bp.load_project()` | ||
| * [x] Improve reserved aminoacid characters | ||
| * [x] Add `SeqFile.max_seq` and `.min_seq` properties | ||
| * [x] Patch `Project` deserializer to improve BioProvDocument creation | ||
| * [x] Make shorter Environment hashes | ||
| * [x] Improve Project `__repr__` | ||
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||
| ### v0.1.22 | ||
| * Simplify `bp.load_project()` function [x] | ||
| * Fix user and env PROV relationships [x] | ||
| * Add Run attributes as Program class properties (will consume from the last run) [x] | ||
| * Add sequence dunder methods for Project class [x] | ||
| * Improve run methods [x] | ||
| * Allow specifying sequence format to PresetProgram outputs [x] | ||
| * Update env file to Py 3.9 [x] | ||
| * [x] Simplify `bp.load_project()` function | ||
| * [x] Fix user and env PROV relationships | ||
| * [x] Add Run attributes as Program class properties (will consume from the last run) | ||
| * [x] Add sequence dunder methods for Project class | ||
| * [x] Improve run methods | ||
| * [x] Allow specifying sequence format to PresetProgram outputs | ||
| * [x] Update env file to Py 3.9 | ||
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||
| ### v0.1.21 | ||
| * Add _config argument to `bp.load_project()` (this is a temporary fix) [x] | ||
| * Add db property to Config class (prevents bug when setting DB path) [x] | ||
| * Improve a few docstrings [x] | ||
| * Refactor sha1 as sha256 [x] | ||
| * Add add and radd dunder methods for Directory and File [x] | ||
| * Package workflows in single module [x] | ||
| * Add FastTree PresetProgram [x] | ||
| * [x] Add _config argument to `bp.load_project()` (this is a temporary fix) | ||
| * [x] Add db property to Config class (prevents bug when setting DB path) | ||
| * [x] Improve a few docstrings | ||
| * [x] Refactor sha1 as sha256 | ||
| * [x] Add add and radd dunder methods for Directory and File | ||
| * [x] Package workflows in single module | ||
| * [x] Add FastTree PresetProgram | ||
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| ### v0.1.20 | ||
| * Debug graphical DOT output [x] | ||
| * Add Muscle PresetProgram [x] | ||
| * Add MAFFT PresetProgram [x] | ||
| * Add Kallisto PresetProgram [x] | ||
| * Add extra_flags attribute to PresetProgram [x] | ||
| * Refactor EnvProv class as Environment [x] | ||
| * Allow creation of users and envs to be optional [x] | ||
| * Create environments only when there's an associated activity [x] | ||
| * Create Sample dunder enter and dunder exit methods [x] | ||
| * Fixing wasDerivedFrom bug when sample and file have same names [x] | ||
| * Fix extra Environments bug [x] | ||
| * [x] Debug graphical DOT output | ||
| * [x] Add Muscle PresetProgram | ||
| * [x] Add MAFFT PresetProgram | ||
| * [x] Add Kallisto PresetProgram | ||
| * [x] Add extra_flags attribute to PresetProgram | ||
| * [x] Refactor EnvProv class as Environment | ||
| * [x] Allow creation of users and envs to be optional | ||
| * [x] Create environments only when there's an associated activity | ||
| * [x] Create Sample dunder enter and dunder exit methods | ||
| * [x] Fixing wasDerivedFrom bug when sample and file have same names | ||
| * [x] Fix extra Environments bug | ||
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| ### v0.1.19 | ||
| * Debug API endpoint (#23) [x] | ||
| * Implement logging [x] | ||
| * Implement Workflow logging [x] | ||
| * Debug Workflow Steps [x] | ||
| * Remove workflow main methods [x] | ||
| * Workflows must now be called only from the CLI [x] | ||
| * Implement post-workflow actions [x] | ||
| * Update db [x] | ||
| * Upload to ProvStore [x] | ||
| * Write PROVN [x] | ||
| * Write PDF [x] | ||
| * Add Sample.auto_update_db() methods [x] | ||
| * Remove logger call when updating Project in database [x] | ||
| * [x] Debug API endpoint (#23) | ||
| * [x] Implement logging | ||
| * [x] Implement Workflow logging | ||
| * [x] Debug Workflow Steps | ||
| * [x] Remove workflow main methods | ||
| * [x] Workflows must now be called only from the CLI | ||
| * [x] Implement post-workflow actions | ||
| * [x] Update db | ||
| * [x] Upload to ProvStore | ||
| * [x] Write PROVN | ||
| * [x] Write PDF | ||
| * [x] Add Sample.auto_update_db() methods | ||
| * [x] Remove logger call when updating Project in database | ||
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| ### v0.1.18a | ||
| * Patch file deserializer bug [x] | ||
| * [x] Patch file deserializer bug | ||
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| ### v0.1.18 | ||
| * Add support for ProvStore API (#23) [x] | ||
| * Add subparsers for CLI commands [x] | ||
| * Add Directories class to Files module [x] | ||
| * Support globbing Directory outputs [x] | ||
| * Increase test coverage [x] | ||
| * Added more example data [x] | ||
| * Make config.threads an integer to support operations [x] | ||
| * [x] Add support for ProvStore API (#23) | ||
| * [x] Add subparsers for CLI commands | ||
| * [x] Add Directories class to Files module | ||
| * [x] Support globbing Directory outputs | ||
| * [x] Increase test coverage | ||
| * [x] Added more example data | ||
| * [x] Make config.threads an integer to support operations | ||
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| ### v0.1.17 | ||
| * Add more database methods [x] | ||
| * Improver error handling for JSON methods [x] | ||
| * Add Project.run_programs method [x] | ||
| * Create ProvEntity and ProvActivity for Project.files and .programs [x] | ||
| * Create Project Bundle for .files and .programs [x] | ||
| * [x] Add more database methods | ||
| * [x] Improver error handling for JSON methods | ||
| * [x] Add Project.run_programs method | ||
| * [x] Create ProvEntity and ProvActivity for Project.files and .programs | ||
| * [x] Create Project Bundle for .files and .programs | ||
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| ### v0.1.16 | ||
| * Update README [x] | ||
| * Add Project.add_files() and add_programs() method [x] | ||
| * Improve Project deserializer [x] | ||
| * Add Project steps to Workflow class [x] | ||
| * [x] Update README | ||
| * [x] Add Project.add_files() and add_programs() method | ||
| * [x] Improve Project deserializer | ||
| * [x] Add Project steps to Workflow class | ||
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| ### v0.1.15 | ||
| * Improve Sample.to_series() and Project.to_csv() methods [x] | ||
| * Add Project.to_csv() calls to tests [x] | ||
| * Add database commands to CLI options [x] | ||
| * Remodel environment as Agent rather than Entity [x] | ||
| * Improve output PROVN documents [x] | ||
| * Add Diamond preset and tests [x] | ||
| * [x] Improve Sample.to_series() and Project.to_csv() methods | ||
| * [x] Add Project.to_csv() calls to tests | ||
| * [x] Add database commands to CLI options | ||
| * [x] Remodel environment as Agent rather than Entity | ||
| * [x] Improve output PROVN documents | ||
| * [x] Add Diamond preset and tests | ||
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| ### v0.1.14 | ||
| * Add blastdb example data [x] | ||
| * Add BLASTn preset and workflow and respective tests [x] | ||
| * Improve BioProvDB tests [x] | ||
| * Improve Project.auto_update and Project.sha1 behaviour and tests [x] | ||
| * Improve Workflow behaviour for custom Workflow arguments [x] | ||
| * [x] Add blastdb example data | ||
| * [x] Add BLASTn preset and workflow and respective tests | ||
| * [x] Improve BioProvDB tests | ||
| * [x] Improve Project.auto_update and Project.sha1 behaviour and tests | ||
| * [x] Improve Workflow behaviour for custom Workflow arguments | ||
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| ### v0.1.13 | ||
| * Add BioProvDB class [x] | ||
| * Add database methods to Project class [x] | ||
| * Add BioProvDB tests [x] | ||
| * Add dot attribute to BioProvDocument [x] | ||
| * Update W3C-PROV tutorial [x] | ||
| * Improve test coverage [x] | ||
| * Debug Program deserializer [x] | ||
| * [x] Add BioProvDB class | ||
| * [x] Add database methods to Project class | ||
| * [x] Add BioProvDB tests | ||
| * [x] Add dot attribute to BioProvDocument | ||
| * [x] Update W3C-PROV tutorial | ||
| * [x] Improve test coverage | ||
| * [x] Debug Program deserializer | ||
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| ### v0.1.12 | ||
| * Patching errors for JSON IO [x] | ||
| * Create File, Program, Run deserializers [x] | ||
| * Implement path replacing methods for multi-user support [x] | ||
| * [x] Patching errors for JSON IO | ||
| * [x] Create File, Program, Run deserializers | ||
| * [x] Implement path replacing methods for multi-user support | ||
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| ### v0.1.11 | ||
| * Fix Run.start_time and Run.end_time testing [x] | ||
| * Improve Program tests [x] | ||
| * Allow users to have multiple environments [x] | ||
| * Improving internal PROV relationships [x] | ||
| * [x] Fix Run.start_time and Run.end_time testing | ||
| * [x] Improve Program tests | ||
| * [x] Allow users to have multiple environments | ||
| * [x] Improving internal PROV relationships | ||
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| ### v0.1.10 | ||
| * Refactoring hashes using hashlib [x] | ||
| * Removing EnvProv.env_set attribute [x] | ||
| * Implementing file hashes [x] | ||
| * Debug EnvProv JSON deserializer [x] | ||
| * Updating introductory tutorial [x] | ||
| * [x] Refactoring hashes using hashlib | ||
| * [x] Removing EnvProv.env_set attribute | ||
| * [x] Implementing file hashes | ||
| * [x] Debug EnvProv JSON deserializer | ||
| * [x] Updating introductory tutorial | ||
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| ### v0.1.9 | ||
| * Improve Env constructor in Project deserializer [x] | ||
| * Improve Program behaviour when dealing with not found Programs [x] | ||
| * Implement utils.serializer_filter function [x] | ||
| * Improve pretty printing of commands [x] | ||
| * [x] Improve Env constructor in Project deserializer | ||
| * [x] Improve Program behaviour when dealing with not found Programs | ||
| * [x] Implement utils.serializer_filter function | ||
| * [x] Improve pretty printing of commands | ||
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| ### v0.1.8 | ||
| * Improve BioProvDocument constructor [x] | ||
| * Improve Sample and Program serializers [x] | ||
| * Improve internal PROV relationships [x] | ||
| * [x] Improve BioProvDocument constructor | ||
| * [x] Improve Sample and Program serializers | ||
| * [x] Improve internal PROV relationships | ||
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| ### v0.1.7 | ||
| * Fix documentation build [x] | ||
| * Refactor f-strings [x] | ||
| * Draft of complete Prov document (all relationships) [x] | ||
| * [x] Fix documentation build | ||
| * [x] Refactor f-strings | ||
| * [x] Draft of complete Prov document (all relationships) | ||
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| ### v0.1.6 | ||
| * Add more Provenance classes [x] | ||
| * Improve Provenance graph [x] | ||
| * Add contributing guidelines [x] | ||
| * Refactor config and prov modules [x] | ||
| * Add CLI options to show config [x] | ||
| * Rename src.program to src.main [x] | ||
| * Refactoring tests: joining src.program and src.sample tests into src.main [x] | ||
| * [x] Add more Provenance classes | ||
| * [x] Improve Provenance graph | ||
| * [x] Add contributing guidelines | ||
| * [x] Refactor config and prov modules | ||
| * [x] Add CLI options to show config | ||
| * [x] Rename src.program to src.main | ||
| * [x] Refactoring tests: joining src.program and src.sample tests into src.main | ||
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| ### v0.1.5 | ||
| * Add W3C-PROV tutorial [x] | ||
| * Small tweaks to default arguments in Program and File module [x] | ||
| * [x] Add W3C-PROV tutorial | ||
| * [x] Small tweaks to default arguments in Program and File module | ||
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| ### v0.1.4 | ||
| * Fix PresetProgram.add_parameter bug [x] | ||
| * Add basic Tutorial [x] | ||
| * Refactor SeqStats data class [x] | ||
| * Improve Provenance classes [x] | ||
| * [x] Fix PresetProgram.add_parameter bug | ||
| * [x] Add basic Tutorial | ||
| * [x] Refactor SeqStats data class | ||
| * [x] Improve Provenance classes | ||
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| ### v0.1.3 | ||
| * Patching more JSON IO bugs [x] | ||
| * [x] Patching more JSON IO bugs | ||
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| ### v0.1.2 | ||
| * Refactor functions in src.files module [x] | ||
| * Add support for BioPython AlignIO module [x] | ||
| * Patching src.program module [x] | ||
| * Improving JSON serializers [x] | ||
| * [x] Refactor functions in src.files module | ||
| * [x] Add support for BioPython AlignIO module | ||
| * [x] Patching src.program module | ||
| * [x] Improving JSON serializers |