pylabrat 0.1__tar.gz

pylabrat-0.1/LICENSE

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+MIT License
+
+Copyright (c) 2018 Shaurita D. Hutchins
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

pylabrat-0.1/MANIFEST.in

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+include tests/
+include labrat/genetics/codons.json
+recursive-include labrat *.json

pylabrat-0.1/PKG-INFO

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+Metadata-Version: 2.4
+Name: pylabrat
+Version: 0.1
+Summary: A package of helpful guis and functions to improve reproducibility for genetics/psychiatry related labs.
+Author-email: Shaurita Hutchins <shaurita.d.hutchins@gmail.com>
+License-Expression: MIT
+Project-URL: Homepage, https://github.com/sdhutchins/labrat
+Project-URL: Documentation, https://labrat.readthedocs.io/en/latest/
+Project-URL: Releases, https://github.com/sdhutchins/labrat/releases
+Project-URL: Issues, https://github.com/sdhutchins/labrat/issues
+Keywords: science,lab,genetics,math,filemanagement
+Classifier: Development Status :: 3 - Alpha
+Classifier: Programming Language :: Python :: 3
+Classifier: Operating System :: POSIX :: Linux
+Classifier: Operating System :: Unix
+Classifier: Natural Language :: English
+Classifier: Programming Language :: Python :: 3 :: Only
+Classifier: Programming Language :: Python :: 3.7
+Classifier: Programming Language :: Python :: 3.8
+Classifier: Programming Language :: Python :: 3.9
+Requires-Python: >=3.7
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: cookiecutter>=1.5.1
+Requires-Dist: logzero>=1.3.1
+Requires-Dist: exmemo>=0.1.0
+Requires-Dist: click>=6.7
+Requires-Dist: jinja2-time>=0.2.0
+Provides-Extra: docs
+Requires-Dist: mkdocs>=1.5.0; extra == "docs"
+Requires-Dist: mkdocs-material>=9.0.0; extra == "docs"
+Requires-Dist: mkdocs-click>=0.8.0; extra == "docs"
+Requires-Dist: mkdocstrings[python]>=0.23.0; extra == "docs"
+Requires-Dist: pymdown-extensions>=10.0.0; extra == "docs"
+Dynamic: license-file
+
+# labrat
+
+[![Build Status](https://app.travis-ci.com/sdhutchins/labrat.svg?token=xfnbNTQhjNbir5xACn8R&branch=master)](https://app.travis-ci.com/sdhutchins/labrat)
+[![codecov](https://codecov.io/gh/sdhutchins/labrat/graph/badge.svg?token=LqA1Lqf0uu)](https://codecov.io/gh/sdhutchins/labrat)
+[![DOI](https://zenodo.org/badge/99277244.svg)](https://doi.org/10.5281/zenodo.17705600)
+
+A basic science lab framework aimed at reproducibility and lab management. This package is in the very early stages of development.
+
+## Features
+
+- Create, list, and track/manage computational biology projects with structured templates
+- Calculate solution dilutions, molarity, transmittance/absorbance conversions, and more
+- Automatically organize scientific data files (FASTQ, FASTA, SAM, BAM, VCF, etc.) and others files like pictures, videos, and archives
+- Archive projects and directories with timestamped backups
+- Convert DNA sequences to amino acids and analyze genetic data
+- Full-featured CLI for all major operations
+
+## Install
+
+Install from PyPI:
+```bash
+pip install pylabrat
+```
+
+Or install from source:
+```bash
+git clone https://github.com/sdhutchins/labrat.git
+cd labrat
+pip install .
+```
+
+For development, install in editable mode:
+```bash
+pip install -e .
+```
+
+## Examples
+
+### Command-Line Interface
+
+Create a new project:
+```bash
+labrat project new --type computational-biology --name "KARG Analysis" \
+  --path ./karg_analysis --description "Analyze the KARG data"
+```
+
+List all projects:
+```bash
+labrat project list
+```
+
+Archive files or directories:
+```bash
+labrat archive --source ./my_project --destination ~/Archive --name "project_backup"
+```
+
+Organize scientific data files:
+```bash
+labrat organize --science
+```
+
+### Python API
+
+Calculate solution dilutions:
+```python
+from labrat.math import dilute_stock
+
+# Calculate final concentration
+final_conc = dilute_stock(100, 2, vF=4)  # Returns 50.0
+```
+
+Manage projects programmatically:
+```python
+from labrat.project import ProjectManager
+
+# Create a new project
+manager = ProjectManager('Dr. Jane Doe')
+manager.new_project(
+    project_type='computational-biology',
+    project_name='KARG Analysis',
+    project_path='./karg_analysis',
+    description="Analyze the KARG data."
+)
+
+# List all projects
+projects = manager.list_projects()
+```
+
+## Tests
+
+Before running tests, ensure all dependencies are installed:
+
+```bash
+pip install -r requirements.txt
+```
+
+Or if installing the package:
+
+```bash
+pip install .
+```
+
+Run all tests using unittest:
+
+```bash
+python -m unittest discover -s tests
+```
+
+Or run tests with pytest (if installed):
+
+```bash
+pytest tests/
+```
+
+To run a specific test file:
+
+```bash
+python -m unittest tests.test_archiver
+python -m unittest tests.test_file_organizer
+python -m unittest tests.test_project_manager
+```
+
+## ToDo
+
+- [ ] Add a lab inventory app
+- [ ] Add project report template
+- [ ] Integrate [exmemo](https://github.com/kalekundert/exmemo)
+
+## Author
+
+Shaurita Hutchins · [@sdhutchins](https://github.com/sdhutchins)
+    · [:email:](mailto:shaurita.d.hutchins@gmail.com)
+
+## Contributing
+
+If you would like to contribute to this package, install the package in
+development mode, and check out our [contributing
+guidelines](https://github.com/sdhutchins/labrat/blob/master/CONTRIBUTING.md).
+
+## License
+
+[MIT](https://github.com/sdhutchins/labrat/blob/master/LICENSE)

pylabrat-0.1/README.md

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+# labrat
+
+[![Build Status](https://app.travis-ci.com/sdhutchins/labrat.svg?token=xfnbNTQhjNbir5xACn8R&branch=master)](https://app.travis-ci.com/sdhutchins/labrat)
+[![codecov](https://codecov.io/gh/sdhutchins/labrat/graph/badge.svg?token=LqA1Lqf0uu)](https://codecov.io/gh/sdhutchins/labrat)
+[![DOI](https://zenodo.org/badge/99277244.svg)](https://doi.org/10.5281/zenodo.17705600)
+
+A basic science lab framework aimed at reproducibility and lab management. This package is in the very early stages of development.
+
+## Features
+
+- Create, list, and track/manage computational biology projects with structured templates
+- Calculate solution dilutions, molarity, transmittance/absorbance conversions, and more
+- Automatically organize scientific data files (FASTQ, FASTA, SAM, BAM, VCF, etc.) and others files like pictures, videos, and archives
+- Archive projects and directories with timestamped backups
+- Convert DNA sequences to amino acids and analyze genetic data
+- Full-featured CLI for all major operations
+
+## Install
+
+Install from PyPI:
+```bash
+pip install pylabrat
+```
+
+Or install from source:
+```bash
+git clone https://github.com/sdhutchins/labrat.git
+cd labrat
+pip install .
+```
+
+For development, install in editable mode:
+```bash
+pip install -e .
+```
+
+## Examples
+
+### Command-Line Interface
+
+Create a new project:
+```bash
+labrat project new --type computational-biology --name "KARG Analysis" \
+  --path ./karg_analysis --description "Analyze the KARG data"
+```
+
+List all projects:
+```bash
+labrat project list
+```
+
+Archive files or directories:
+```bash
+labrat archive --source ./my_project --destination ~/Archive --name "project_backup"
+```
+
+Organize scientific data files:
+```bash
+labrat organize --science
+```
+
+### Python API
+
+Calculate solution dilutions:
+```python
+from labrat.math import dilute_stock
+
+# Calculate final concentration
+final_conc = dilute_stock(100, 2, vF=4)  # Returns 50.0
+```
+
+Manage projects programmatically:
+```python
+from labrat.project import ProjectManager
+
+# Create a new project
+manager = ProjectManager('Dr. Jane Doe')
+manager.new_project(
+    project_type='computational-biology',
+    project_name='KARG Analysis',
+    project_path='./karg_analysis',
+    description="Analyze the KARG data."
+)
+
+# List all projects
+projects = manager.list_projects()
+```
+
+## Tests
+
+Before running tests, ensure all dependencies are installed:
+
+```bash
+pip install -r requirements.txt
+```
+
+Or if installing the package:
+
+```bash
+pip install .
+```
+
+Run all tests using unittest:
+
+```bash
+python -m unittest discover -s tests
+```
+
+Or run tests with pytest (if installed):
+
+```bash
+pytest tests/
+```
+
+To run a specific test file:
+
+```bash
+python -m unittest tests.test_archiver
+python -m unittest tests.test_file_organizer
+python -m unittest tests.test_project_manager
+```
+
+## ToDo
+
+- [ ] Add a lab inventory app
+- [ ] Add project report template
+- [ ] Integrate [exmemo](https://github.com/kalekundert/exmemo)
+
+## Author
+
+Shaurita Hutchins · [@sdhutchins](https://github.com/sdhutchins)
+    · [:email:](mailto:shaurita.d.hutchins@gmail.com)
+
+## Contributing
+
+If you would like to contribute to this package, install the package in
+development mode, and check out our [contributing
+guidelines](https://github.com/sdhutchins/labrat/blob/master/CONTRIBUTING.md).
+
+## License
+
+[MIT](https://github.com/sdhutchins/labrat/blob/master/LICENSE)

pylabrat-0.1/labrat/__init__.py

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+# Package Global Variables
+_DATEFMT1 = '%a %b %d %I:%M:%S %p %Y'  # Used to add as a date
+_DATEFMT2 = '%m-%d-%Y_%I-%M-%S-%p'  # Used to append to archives

pylabrat-0.1/labrat/cli.py

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+# -*- coding: utf-8 -*-
+"""Command-line interface for labrat."""
+import click
+from pathlib import Path
+from labrat.project import ProjectManager
+from labrat.filemanager import Archiver, FileOrganizer
+
+
+@click.group()
+def main():
+    """Labrat - A basic science lab framework for reproducibility and lab management."""
+    pass
+
+
+@main.group()
+def project():
+    """Manage projects."""
+    pass
+
+
+@project.command('new')
+@click.option('--type', 'project_type', required=True,
+              help='Type of project (e.g., computational-biology, data-science)')
+@click.option('--name', 'project_name', required=True,
+              help='Name of the project')
+@click.option('--path', 'project_path', required=True, type=click.Path(),
+              help='Path where the project will be created')
+@click.option('--description', required=True,
+              help='Description of the project')
+@click.option('--username', default=None,
+              help='Username for project manager (defaults to system default)')
+def new_project(project_type, project_name, project_path, description, username):
+    """Create a new project."""
+    try:
+        manager = ProjectManager(username=username)
+        manager.new_project(
+            project_type=project_type,
+            project_name=project_name,
+            project_path=project_path,
+            description=description
+        )
+        click.echo(f"✓ Project '{project_name}' created successfully at {project_path}")
+    except Exception as e:
+        click.echo(f"✗ Error creating project: {e}", err=True)
+        raise click.Abort()
+
+
+@project.command('list')
+@click.option('--username', default=None,
+              help='Username for project manager (defaults to system default)')
+def list_projects(username):
+    """List all projects."""
+    try:
+        manager = ProjectManager(username=username)
+        projects = manager.list_projects()
+        
+        if not projects:
+            click.echo("No projects found.")
+            return
+        
+        click.echo(f"\nFound {len(projects)} project(s):\n")
+        for idx, proj in enumerate(projects, 1):
+            click.echo(f"{idx}. {proj.get('name', 'Unknown')}")
+            click.echo(f"   Path: {proj.get('path', 'Unknown')}")
+            click.echo(f"   Type: {proj.get('project_type', 'Unknown')}")
+            click.echo(f"   Created: {proj.get('created_at', 'Unknown')}")
+            click.echo()
+    except Exception as e:
+        click.echo(f"✗ Error listing projects: {e}", err=True)
+        raise click.Abort()
+
+
+@project.command('delete')
+@click.option('--path', 'project_path', required=True, type=click.Path(exists=True),
+              help='Path to the project to delete')
+@click.option('--archive-dir', required=True, type=click.Path(),
+              help='Directory where the archived project will be stored')
+@click.option('--username', default=None,
+              help='Username for project manager (defaults to system default)')
+@click.confirmation_option(prompt='Are you sure you want to delete this project?')
+def delete_project(project_path, archive_dir, username):
+    """Delete a project (archives it first)."""
+    try:
+        manager = ProjectManager(username=username)
+        archive_path = manager.delete_project(project_path, archive_dir)
+        click.echo(f"✓ Project deleted and archived to: {archive_path}")
+    except Exception as e:
+        click.echo(f"✗ Error deleting project: {e}", err=True)
+        raise click.Abort()
+
+
+@main.command('archive')
+@click.option('--source', required=True, type=click.Path(exists=True, dir_okay=True),
+              help='Source directory to archive')
+@click.option('--destination', required=True, type=click.Path(),
+              help='Base directory for storing archives')
+@click.option('--name', 'project_name', required=True,
+              help='Name for the archive')
+def archive(source, destination, project_name):
+    """Archive a directory."""
+    try:
+        archive_dir = Archiver.get_archive_dir(destination, project_name)
+        archiver = Archiver(source_dir=source, archive_dir=archive_dir)
+        zip_path = archiver.archive()
+        click.echo(f"✓ Archive created successfully: {zip_path}")
+    except Exception as e:
+        click.echo(f"✗ Error creating archive: {e}", err=True)
+        raise click.Abort()
+
+
+@main.command('organize')
+@click.option('--science', 'organize_science', is_flag=True,
+              help='Organize scientific data files (fastq, fasta, sam, bam, vcf, fits, hdf5, etc.) to Documents/Research_Data')
+@click.option('--science-dir', type=click.Path(),
+              help='Custom directory for scientific data files (default: Documents/Research_Data)')
+@click.option('--keyword', default=None,
+              help='Move files containing this keyword to a specific folder')
+@click.option('--pictures', 'organize_pictures', is_flag=True,
+              help='Organize picture files to Pictures folder')
+@click.option('--videos', 'organize_videos', is_flag=True,
+              help='Organize video files to Videos folder')
+@click.option('--archives', 'organize_archives', is_flag=True,
+              help='Organize archive files by compression type')
+@click.option('--all', 'organize_all', is_flag=True,
+              help='Organize all file types')
+def organize(organize_science, science_dir, keyword, organize_pictures,
+             organize_videos, organize_archives, organize_all):
+    """
+    Organize files in Downloads and Documents directories.
+    
+    By default, scientific data files (fastq, fasta, sam, bam, vcf, fits, hdf5, nc, etc.)
+    are moved to Documents/Research_Data. Use --science-dir to specify a custom location.
+    
+    Examples:
+        labrat organize --science
+        labrat organize --science --science-dir ~/Research
+        labrat organize --keyword "project_alpha"
+        labrat organize --all
+    """
+    if not any([organize_science, keyword, organize_pictures, organize_videos,
+                organize_archives, organize_all]):
+        click.echo("Error: Specify at least one organization option", err=True)
+        click.echo("Use --science to organize science files, or --all for everything", err=True)
+        raise click.Abort()
+    
+    try:
+        organizer = FileOrganizer()
+        actions_taken = []
+        
+        if organize_all:
+            organizer.organize_all()
+            actions_taken.append("all files")
+        else:
+            # Organize science files (default behavior for scientists)
+            if organize_science:
+                organizer.organize_science_files(science_dir=science_dir)
+                location = science_dir if science_dir else "Documents/Research_Data"
+                actions_taken.append(f"science files to {location}")
+            
+            # Organize media files
+            if organize_pictures or organize_videos:
+                organizer.organize_files()
+                media = []
+                if organize_pictures:
+                    media.append("pictures")
+                if organize_videos:
+                    media.append("videos")
+                actions_taken.append(f"{' and '.join(media)}")
+            
+            # Organize archives
+            if organize_archives:
+                organizer.organize_archives()
+                actions_taken.append("archives")
+            
+            # Handle keyword-based organization
+            if keyword:
+                organizer.move_specific_files(keyword=keyword)
+                actions_taken.append(f"files with keyword '{keyword}'")
+        
+        click.echo(f"✓ Organized {', '.join(actions_taken)} successfully")
+    except Exception as e:
+        click.echo(f"✗ Error organizing files: {e}", err=True)
+        raise click.Abort()
+
+
+if __name__ == "__main__":
+    main()

pylabrat-0.1/labrat/filemanager/__init__.py

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+from .archive import Archiver
+from .organize import FileOrganizer

pylabrat-0.1/labrat/filemanager/archive.py

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+from shutil import copytree, SameFileError, make_archive
+from datetime import datetime
+from pathlib import Path
+import logzero
+from logzero import logger
+from labrat.utils import get_labrat_dir
+
+
+class Archiver:
+    """Archive folders and files."""
+
+    def __init__(self, source_dir, archive_dir):
+        """
+        Initialize logger and archive parameters.
+
+        Args:
+            source_dir (str or Path): The directory to copy or archive.
+            archive_dir (str or Path): The destination directory for the archive.
+        """
+        self.source_dir = Path(source_dir).resolve()
+        self.archive_dir = Path(archive_dir).resolve()
+
+        if not self.source_dir.exists() or not self.source_dir.is_dir():
+            raise ValueError(f"Source directory '{self.source_dir}' does not exist or is not a directory.")
+        logger.debug(f"Source directory: {self.source_dir}")
+
+        if not self.archive_dir.parent.exists():
+            raise ValueError(f"Archive directory parent '{self.archive_dir.parent}' does not exist.")
+        logger.debug(f"Archive directory: {self.archive_dir}")
+
+        # Configure log file in .labrat directory
+        # Store logs in user's home directory under .labrat folder
+        labrat_dir = get_labrat_dir()
+        log_file = labrat_dir / f"archive_{datetime.now().strftime('%Y%m%d_%H%M%S')}.log"
+        logzero.logfile(str(log_file))
+        logger.info("Archive initialized.")
+
+    def archive(self):
+        """
+        Perform the archive by copying the source directory to the archive directory
+        and then creating a zip file of the archived folder.
+
+        Raises:
+            SameFileError: If the source and destination are the same.
+            OSError: For other filesystem-related errors.
+        """
+        logger.info("Starting archive process...")
+        logger.info(f"Source: {self.source_dir}")
+        logger.info(f"Destination: {self.archive_dir}")
+
+        # Step 1: Copy the source directory to the archive directory
+        try:
+            copytree(self.source_dir, self.archive_dir)
+            logger.info(f"Archive folder created successfully: {self.source_dir} -> {self.archive_dir}")
+        except SameFileError as e:
+            logger.error(f"Source and destination are the same: {e}")
+            raise
+        except FileExistsError:
+            logger.warning(f"Archive destination already exists: {self.archive_dir}")
+        except OSError as e:
+            logger.error(f"Failed to complete archive: {e}")
+            raise
+
+        # Create a zip file for the archived folder
+        try:
+            zip_path = make_archive(
+                base_name=str(self.archive_dir),  # The base name of the archive
+                format="zip",                     # Archive format
+                root_dir=str(self.archive_dir),   # Root directory to archive
+            )
+            logger.info(f"Archive zipped successfully: {zip_path}")
+        except OSError as e:
+            logger.error(f"Failed to zip the archive: {e}")
+            raise
+
+        return zip_path
+
+    @staticmethod
+    def get_archive_dir(base_dir, project_name):
+        """
+        Generate a timestamped archive directory path.
+
+        Args:
+            base_dir (str or Path): The base directory where archives are stored.
+            project_name (str): The name of the project being archived.
+
+        Returns:
+            Path: A path to the timestamped archive directory.
+        """
+        base_dir = Path(base_dir).resolve()
+        timestamp = datetime.now().strftime("%Y%m%d_%H%M%S")
+        archive_dir = base_dir / f"{project_name}_archive_{timestamp}"
+        logger.debug(f"Generated archive directory: {archive_dir}")
+        return archive_dir