v2.4.9

CHANGELOG

v2.1.0 (2025-04-30)

Chores

• Add runtime analysis
  (1847ea2)

Features

• Add runtime comparison script
  (36775ed)

Refactoring

• Ensure database path exists
  (283ecb0)

• Fix parameter
  (35c2621)

• Remove threads
  (c42db6d)

v2.0.6 (2025-04-29)

Bug Fixes

• Make database more robust for jupyter notebook
  (804a8ff)

Chores

• Add UniProt projection example tailed for Colab experience
  (#12,
  e287d01)

Summary This PR significantly improves the aesthetics and user experience of the

uniprot_projection.py example when viewed as a Google Colab notebook. The changes focus on visual
enhancements and interactive elements while maintaining the same functionality. ## Changes - Added
styled section headers with custom backgrounds and borders - Implemented interactive progress bars
for processing steps - Added color-coded status messages with appropriate icons (✅, ⚠️, ℹ️, ❌) -
Improved error and warning displays with formatted message boxes - Enhanced SVG display with
additional protein information card - Added visual feedback during long-running operations -
Improved configuration display with formatted tables - Added completion banner at the end of
execution - Added professional footer with attribution - Fixed cell structure for proper Colab
execution

Motivation The notebook acts as a demonstration tool for FlatProt functionality. These visual

enhancements make it more professional-looking and easier to follow for users exploring the tool
through Colab. The interactive elements also provide better feedback during execution.

Testing Tested in Google Colab environment to ensure all visual enhancements render correctly and

all functionality remains intact.

• Fix foldseek command test
  (b88a168)

Documentation

• Add better workflow description
  (8dc7a0a)

• Add PR rule to cursorrules
  (0457605)

Refactoring

• Add forced yes and update UniprotID
  (b5ae58d)

• Add library install as well
  (c246b8b)

• Change to atomic command
  (5731223)

• Fix syntax issue
  (d765ea3)

• Improve notebook style
  (395975c)

• Make download jupyter compatible
  (be416af)

• Pipe yes
  (db5a8ce)

• Remove -qq issue
  (1385248)

• Remove potentially problematic quiet
  (e730e9c)

• Revert to debian non-interactive
  (73c0057)

• Shell dssp
  (7019339)

• Switch to uv install
  (3a3f6cf)

v2.0.5 (2025-04-28)

Bug Fixes

• Refactor DB utils and update examples
  (84abd4d)

This PR introduces several improvements to the handling of the alignment database and updates the
chainsaw.py example accordingly. Key Changes: Database Utilities (src/flatprot/utils/database.py):
Refactored DEFAULT_DB_DIR to use platformdirs for a standard, cross-platform data location
(rostlab/flatprot). Updated DEFAULT_DB_URL to point to the correct Zenodo archive
(alignment_db.zip). Added verify=False to the httpx client during download to mitigate potential
SSL certificate verification errors (includes a warning log). Improved the archive extraction
logic in download_database to: Extract to a temporary location. Specifically look for the
alignment_db folder within the archive. Move the contents of alignment_db to the final target
directory. Ignore other files/folders in the archive (like __MACOSX). Adjusted logging levels for
better clarity during download/extraction. Chainsaw Example (examples/chainsaw.py): Updated the
script to use the new flatprot.utils.database.ensure_database_available function to locate or
download the alignment database, removing hardcoded paths. Commented out Colab-specific shell
commands (!pip, !wget, etc.) to resolve linter errors and ensure the file is valid Python syntax.
Added the missing import for ensure_database_available. Motivation: To make the alignment database
download and storage more robust and platform-independent. To resolve issues related to SSL
verification and archive structure during database download. To ensure the example script utilizes
the centralized database handling logic. To fix linter errors in the example script.

Chores

• Remove CNAME
  (8ac9db4)

• Update connector color
  (979fe58)

v2.0.4 (2025-04-28)

Bug Fixes

• Documentation updates
  (9cd4af7)

v2.0.3 (2025-04-28)

Continuous Integration

• Simplify release config
  (0d929c3)

• Update mkdocs command
  (6cd2768)

v2.0.2 (2025-04-28)

Chores

• Generate example notebooks (#9,
  31ec311)

Automated generation of Jupyter notebooks from example Python scripts. Changes detected in
examples/*.py.

Co-authored-by: t03i t03i@users.noreply.github.com

Continuous Integration

• Add deps to docs-release
  (c4bfb08)

• Add labels permission
  (4fb5d23)

• Add repo checkout to finalize-release
  (41885a6)

• Update notebook pull request
  (d23e6b6)

• Update pull request permissions
  (c4ad0dc)

Documentation

• Update README
  (ee64954)

v2.0.1 (2025-04-22)

v2.0.0 (2025-04-22)

Bug Fixes

• Add - to allow for negative coords
  (f4df4a0)

• Add connection styles
  (771c228)

• Add opacity drawing
  (2d54351)

• Better checkpoint usage
  (a1f1f0c)

• Connection calculation
  (5a6b9ab)

• Dix dssp parsing
  (ed3fc37)

• Filter for target db now working
  (27b12c6)

• Import issues
  (563ba83)

• Improve error handling in alignment and transformation matrix
  (466356e)

• Enhanced error handling in the align_structure_rotation function by reintroducing specific
  handling for FlatProtError, ensuring consistent logging of error messages. - Added validation
  checks in the from_array and from_string methods of the TransformationMatrix class to ensure
  input arrays conform to expected dimensions, raising appropriate ValueError exceptions when
  necessary. - Updated docstrings for clarity and compliance with PEP257.

• Improve error handling in SVG rendering process
  (f1b310d)

• Wrapped the SVG rendering and saving logic in a try...except block to capture and log errors
  during the ...

v2.4.8

CHANGELOG

v2.1.0 (2025-04-30)

Chores

• Add runtime analysis
  (1847ea2)

Features

• Add runtime comparison script
  (36775ed)

Refactoring

• Ensure database path exists
  (283ecb0)

• Fix parameter
  (35c2621)

• Remove threads
  (c42db6d)

v2.0.6 (2025-04-29)

Bug Fixes

• Make database more robust for jupyter notebook
  (804a8ff)

Chores

• Add UniProt projection example tailed for Colab experience
  (#12,
  e287d01)

Summary This PR significantly improves the aesthetics and user experience of the

uniprot_projection.py example when viewed as a Google Colab notebook. The changes focus on visual
enhancements and interactive elements while maintaining the same functionality. ## Changes - Added
styled section headers with custom backgrounds and borders - Implemented interactive progress bars
for processing steps - Added color-coded status messages with appropriate icons (✅, ⚠️, ℹ️, ❌) -
Improved error and warning displays with formatted message boxes - Enhanced SVG display with
additional protein information card - Added visual feedback during long-running operations -
Improved configuration display with formatted tables - Added completion banner at the end of
execution - Added professional footer with attribution - Fixed cell structure for proper Colab
execution

Motivation The notebook acts as a demonstration tool for FlatProt functionality. These visual

enhancements make it more professional-looking and easier to follow for users exploring the tool
through Colab. The interactive elements also provide better feedback during execution.

Testing Tested in Google Colab environment to ensure all visual enhancements render correctly and

all functionality remains intact.

• Fix foldseek command test
  (b88a168)

Documentation

• Add better workflow description
  (8dc7a0a)

• Add PR rule to cursorrules
  (0457605)

Refactoring

• Add forced yes and update UniprotID
  (b5ae58d)

• Add library install as well
  (c246b8b)

• Change to atomic command
  (5731223)

• Fix syntax issue
  (d765ea3)

• Improve notebook style
  (395975c)

• Make download jupyter compatible
  (be416af)

• Pipe yes
  (db5a8ce)

• Remove -qq issue
  (1385248)

• Remove potentially problematic quiet
  (e730e9c)

• Revert to debian non-interactive
  (73c0057)

• Shell dssp
  (7019339)

• Switch to uv install
  (3a3f6cf)

v2.0.5 (2025-04-28)

Bug Fixes

• Refactor DB utils and update examples
  (84abd4d)

This PR introduces several improvements to the handling of the alignment database and updates the
chainsaw.py example accordingly. Key Changes: Database Utilities (src/flatprot/utils/database.py):
Refactored DEFAULT_DB_DIR to use platformdirs for a standard, cross-platform data location
(rostlab/flatprot). Updated DEFAULT_DB_URL to point to the correct Zenodo archive
(alignment_db.zip). Added verify=False to the httpx client during download to mitigate potential
SSL certificate verification errors (includes a warning log). Improved the archive extraction
logic in download_database to: Extract to a temporary location. Specifically look for the
alignment_db folder within the archive. Move the contents of alignment_db to the final target
directory. Ignore other files/folders in the archive (like __MACOSX). Adjusted logging levels for
better clarity during download/extraction. Chainsaw Example (examples/chainsaw.py): Updated the
script to use the new flatprot.utils.database.ensure_database_available function to locate or
download the alignment database, removing hardcoded paths. Commented out Colab-specific shell
commands (!pip, !wget, etc.) to resolve linter errors and ensure the file is valid Python syntax.
Added the missing import for ensure_database_available. Motivation: To make the alignment database
download and storage more robust and platform-independent. To resolve issues related to SSL
verification and archive structure during database download. To ensure the example script utilizes
the centralized database handling logic. To fix linter errors in the example script.

Chores

• Remove CNAME
  (8ac9db4)

• Update connector color
  (979fe58)

v2.0.4 (2025-04-28)

Bug Fixes

• Documentation updates
  (9cd4af7)

v2.0.3 (2025-04-28)

Continuous Integration

• Simplify release config
  (0d929c3)

• Update mkdocs command
  (6cd2768)

v2.0.2 (2025-04-28)

Chores

• Generate example notebooks (#9,
  31ec311)

Automated generation of Jupyter notebooks from example Python scripts. Changes detected in
examples/*.py.

Co-authored-by: t03i t03i@users.noreply.github.com

Continuous Integration

• Add deps to docs-release
  (c4bfb08)

• Add labels permission
  (4fb5d23)

• Add repo checkout to finalize-release
  (41885a6)

• Update notebook pull request
  (d23e6b6)

• Update pull request permissions
  (c4ad0dc)

Documentation

• Update README
  (ee64954)

v2.0.1 (2025-04-22)

v2.0.0 (2025-04-22)

Bug Fixes

• Add - to allow for negative coords
  (f4df4a0)

• Add connection styles
  (771c228)

• Add opacity drawing
  (2d54351)

• Better checkpoint usage
  (a1f1f0c)

• Connection calculation
  (5a6b9ab)

• Dix dssp parsing
  (ed3fc37)

• Filter for target db now working
  (27b12c6)

• Import issues
  (563ba83)

• Improve error handling in alignment and transformation matrix
  (466356e)

• Enhanced error handling in the align_structure_rotation function by reintroducing specific
  handling for FlatProtError, ensuring consistent logging of error messages. - Added validation
  checks in the from_array and from_string methods of the TransformationMatrix class to ensure
  input arrays conform to expected dimensions, raising appropriate ValueError exceptions when
  necessary. - Updated docstrings for clarity and compliance with PEP257.

• Improve error handling in SVG rendering process
  (f1b310d)

• Wrapped the SVG rendering and saving logic in a try...except block to capture and log errors
  during the ...

v2.4.7

CHANGELOG

v2.1.0 (2025-04-30)

Chores

• Add runtime analysis
  (1847ea2)

Features

• Add runtime comparison script
  (36775ed)

Refactoring

• Ensure database path exists
  (283ecb0)

• Fix parameter
  (35c2621)

• Remove threads
  (c42db6d)

v2.0.6 (2025-04-29)

Bug Fixes

• Make database more robust for jupyter notebook
  (804a8ff)

Chores

• Add UniProt projection example tailed for Colab experience
  (#12,
  e287d01)

Summary This PR significantly improves the aesthetics and user experience of the

uniprot_projection.py example when viewed as a Google Colab notebook. The changes focus on visual
enhancements and interactive elements while maintaining the same functionality. ## Changes - Added
styled section headers with custom backgrounds and borders - Implemented interactive progress bars
for processing steps - Added color-coded status messages with appropriate icons (✅, ⚠️, ℹ️, ❌) -
Improved error and warning displays with formatted message boxes - Enhanced SVG display with
additional protein information card - Added visual feedback during long-running operations -
Improved configuration display with formatted tables - Added completion banner at the end of
execution - Added professional footer with attribution - Fixed cell structure for proper Colab
execution

Motivation The notebook acts as a demonstration tool for FlatProt functionality. These visual

enhancements make it more professional-looking and easier to follow for users exploring the tool
through Colab. The interactive elements also provide better feedback during execution.

Testing Tested in Google Colab environment to ensure all visual enhancements render correctly and

all functionality remains intact.

• Fix foldseek command test
  (b88a168)

Documentation

• Add better workflow description
  (8dc7a0a)

• Add PR rule to cursorrules
  (0457605)

Refactoring

• Add forced yes and update UniprotID
  (b5ae58d)

• Add library install as well
  (c246b8b)

• Change to atomic command
  (5731223)

• Fix syntax issue
  (d765ea3)

• Improve notebook style
  (395975c)

• Make download jupyter compatible
  (be416af)

• Pipe yes
  (db5a8ce)

• Remove -qq issue
  (1385248)

• Remove potentially problematic quiet
  (e730e9c)

• Revert to debian non-interactive
  (73c0057)

• Shell dssp
  (7019339)

• Switch to uv install
  (3a3f6cf)

v2.0.5 (2025-04-28)

Bug Fixes

• Refactor DB utils and update examples
  (84abd4d)

This PR introduces several improvements to the handling of the alignment database and updates the
chainsaw.py example accordingly. Key Changes: Database Utilities (src/flatprot/utils/database.py):
Refactored DEFAULT_DB_DIR to use platformdirs for a standard, cross-platform data location
(rostlab/flatprot). Updated DEFAULT_DB_URL to point to the correct Zenodo archive
(alignment_db.zip). Added verify=False to the httpx client during download to mitigate potential
SSL certificate verification errors (includes a warning log). Improved the archive extraction
logic in download_database to: Extract to a temporary location. Specifically look for the
alignment_db folder within the archive. Move the contents of alignment_db to the final target
directory. Ignore other files/folders in the archive (like __MACOSX). Adjusted logging levels for
better clarity during download/extraction. Chainsaw Example (examples/chainsaw.py): Updated the
script to use the new flatprot.utils.database.ensure_database_available function to locate or
download the alignment database, removing hardcoded paths. Commented out Colab-specific shell
commands (!pip, !wget, etc.) to resolve linter errors and ensure the file is valid Python syntax.
Added the missing import for ensure_database_available. Motivation: To make the alignment database
download and storage more robust and platform-independent. To resolve issues related to SSL
verification and archive structure during database download. To ensure the example script utilizes
the centralized database handling logic. To fix linter errors in the example script.

Chores

• Remove CNAME
  (8ac9db4)

• Update connector color
  (979fe58)

v2.0.4 (2025-04-28)

Bug Fixes

• Documentation updates
  (9cd4af7)

v2.0.3 (2025-04-28)

Continuous Integration

• Simplify release config
  (0d929c3)

• Update mkdocs command
  (6cd2768)

v2.0.2 (2025-04-28)

Chores

• Generate example notebooks (#9,
  31ec311)

Automated generation of Jupyter notebooks from example Python scripts. Changes detected in
examples/*.py.

Co-authored-by: t03i t03i@users.noreply.github.com

Continuous Integration

• Add deps to docs-release
  (c4bfb08)

• Add labels permission
  (4fb5d23)

• Add repo checkout to finalize-release
  (41885a6)

• Update notebook pull request
  (d23e6b6)

• Update pull request permissions
  (c4ad0dc)

Documentation

• Update README
  (ee64954)

v2.0.1 (2025-04-22)

v2.0.0 (2025-04-22)

Bug Fixes

• Add - to allow for negative coords
  (f4df4a0)

• Add connection styles
  (771c228)

• Add opacity drawing
  (2d54351)

• Better checkpoint usage
  (a1f1f0c)

• Connection calculation
  (5a6b9ab)

• Dix dssp parsing
  (ed3fc37)

• Filter for target db now working
  (27b12c6)

• Import issues
  (563ba83)

• Improve error handling in alignment and transformation matrix
  (466356e)

• Enhanced error handling in the align_structure_rotation function by reintroducing specific
  handling for FlatProtError, ensuring consistent logging of error messages. - Added validation
  checks in the from_array and from_string methods of the TransformationMatrix class to ensure
  input arrays conform to expected dimensions, raising appropriate ValueError exceptions when
  necessary. - Updated docstrings for clarity and compliance with PEP257.

• Improve error handling in SVG rendering process
  (f1b310d)

• Wrapped the SVG rendering and saving logic in a try...except block to capture and log errors
  during the ...

v2.4.6

CHANGELOG

v2.1.0 (2025-04-30)

Chores

• Add runtime analysis
  (1847ea2)

Features

• Add runtime comparison script
  (36775ed)

Refactoring

• Ensure database path exists
  (283ecb0)

• Fix parameter
  (35c2621)

• Remove threads
  (c42db6d)

v2.0.6 (2025-04-29)

Bug Fixes

• Make database more robust for jupyter notebook
  (804a8ff)

Chores

• Add UniProt projection example tailed for Colab experience
  (#12,
  e287d01)

Summary This PR significantly improves the aesthetics and user experience of the

uniprot_projection.py example when viewed as a Google Colab notebook. The changes focus on visual
enhancements and interactive elements while maintaining the same functionality. ## Changes - Added
styled section headers with custom backgrounds and borders - Implemented interactive progress bars
for processing steps - Added color-coded status messages with appropriate icons (✅, ⚠️, ℹ️, ❌) -
Improved error and warning displays with formatted message boxes - Enhanced SVG display with
additional protein information card - Added visual feedback during long-running operations -
Improved configuration display with formatted tables - Added completion banner at the end of
execution - Added professional footer with attribution - Fixed cell structure for proper Colab
execution

Motivation The notebook acts as a demonstration tool for FlatProt functionality. These visual

enhancements make it more professional-looking and easier to follow for users exploring the tool
through Colab. The interactive elements also provide better feedback during execution.

Testing Tested in Google Colab environment to ensure all visual enhancements render correctly and

all functionality remains intact.

• Fix foldseek command test
  (b88a168)

Documentation

• Add better workflow description
  (8dc7a0a)

• Add PR rule to cursorrules
  (0457605)

Refactoring

• Add forced yes and update UniprotID
  (b5ae58d)

• Add library install as well
  (c246b8b)

• Change to atomic command
  (5731223)

• Fix syntax issue
  (d765ea3)

• Improve notebook style
  (395975c)

• Make download jupyter compatible
  (be416af)

• Pipe yes
  (db5a8ce)

• Remove -qq issue
  (1385248)

• Remove potentially problematic quiet
  (e730e9c)

• Revert to debian non-interactive
  (73c0057)

• Shell dssp
  (7019339)

• Switch to uv install
  (3a3f6cf)

v2.0.5 (2025-04-28)

Bug Fixes

• Refactor DB utils and update examples
  (84abd4d)

This PR introduces several improvements to the handling of the alignment database and updates the
chainsaw.py example accordingly. Key Changes: Database Utilities (src/flatprot/utils/database.py):
Refactored DEFAULT_DB_DIR to use platformdirs for a standard, cross-platform data location
(rostlab/flatprot). Updated DEFAULT_DB_URL to point to the correct Zenodo archive
(alignment_db.zip). Added verify=False to the httpx client during download to mitigate potential
SSL certificate verification errors (includes a warning log). Improved the archive extraction
logic in download_database to: Extract to a temporary location. Specifically look for the
alignment_db folder within the archive. Move the contents of alignment_db to the final target
directory. Ignore other files/folders in the archive (like __MACOSX). Adjusted logging levels for
better clarity during download/extraction. Chainsaw Example (examples/chainsaw.py): Updated the
script to use the new flatprot.utils.database.ensure_database_available function to locate or
download the alignment database, removing hardcoded paths. Commented out Colab-specific shell
commands (!pip, !wget, etc.) to resolve linter errors and ensure the file is valid Python syntax.
Added the missing import for ensure_database_available. Motivation: To make the alignment database
download and storage more robust and platform-independent. To resolve issues related to SSL
verification and archive structure during database download. To ensure the example script utilizes
the centralized database handling logic. To fix linter errors in the example script.

Chores

• Remove CNAME
  (8ac9db4)

• Update connector color
  (979fe58)

v2.0.4 (2025-04-28)

Bug Fixes

• Documentation updates
  (9cd4af7)

v2.0.3 (2025-04-28)

Continuous Integration

• Simplify release config
  (0d929c3)

• Update mkdocs command
  (6cd2768)

v2.0.2 (2025-04-28)

Chores

• Generate example notebooks (#9,
  31ec311)

Automated generation of Jupyter notebooks from example Python scripts. Changes detected in
examples/*.py.

Co-authored-by: t03i t03i@users.noreply.github.com

Continuous Integration

• Add deps to docs-release
  (c4bfb08)

• Add labels permission
  (4fb5d23)

• Add repo checkout to finalize-release
  (41885a6)

• Update notebook pull request
  (d23e6b6)

• Update pull request permissions
  (c4ad0dc)

Documentation

• Update README
  (ee64954)

v2.0.1 (2025-04-22)

v2.0.0 (2025-04-22)

Bug Fixes

• Add - to allow for negative coords
  (f4df4a0)

• Add connection styles
  (771c228)

• Add opacity drawing
  (2d54351)

• Better checkpoint usage
  (a1f1f0c)

• Connection calculation
  (5a6b9ab)

• Dix dssp parsing
  (ed3fc37)

• Filter for target db now working
  (27b12c6)

• Import issues
  (563ba83)

• Improve error handling in alignment and transformation matrix
  (466356e)

• Enhanced error handling in the align_structure_rotation function by reintroducing specific
  handling for FlatProtError, ensuring consistent logging of error messages. - Added validation
  checks in the from_array and from_string methods of the TransformationMatrix class to ensure
  input arrays conform to expected dimensions, raising appropriate ValueError exceptions when
  necessary. - Updated docstrings for clarity and compliance with PEP257.

• Improve error handling in SVG rendering process
  (f1b310d)

• Wrapped the SVG rendering and saving logic in a try...except block to capture and log errors
  during the ...

v2.4.5

CHANGELOG

v2.1.0 (2025-04-30)

Chores

• Add runtime analysis
  (1847ea2)

Features

• Add runtime comparison script
  (36775ed)

Refactoring

• Ensure database path exists
  (283ecb0)

• Fix parameter
  (35c2621)

• Remove threads
  (c42db6d)

v2.0.6 (2025-04-29)

Bug Fixes

• Make database more robust for jupyter notebook
  (804a8ff)

Chores

• Add UniProt projection example tailed for Colab experience
  (#12,
  e287d01)

Summary This PR significantly improves the aesthetics and user experience of the

uniprot_projection.py example when viewed as a Google Colab notebook. The changes focus on visual
enhancements and interactive elements while maintaining the same functionality. ## Changes - Added
styled section headers with custom backgrounds and borders - Implemented interactive progress bars
for processing steps - Added color-coded status messages with appropriate icons (✅, ⚠️, ℹ️, ❌) -
Improved error and warning displays with formatted message boxes - Enhanced SVG display with
additional protein information card - Added visual feedback during long-running operations -
Improved configuration display with formatted tables - Added completion banner at the end of
execution - Added professional footer with attribution - Fixed cell structure for proper Colab
execution

Motivation The notebook acts as a demonstration tool for FlatProt functionality. These visual

enhancements make it more professional-looking and easier to follow for users exploring the tool
through Colab. The interactive elements also provide better feedback during execution.

Testing Tested in Google Colab environment to ensure all visual enhancements render correctly and

all functionality remains intact.

• Fix foldseek command test
  (b88a168)

Documentation

• Add better workflow description
  (8dc7a0a)

• Add PR rule to cursorrules
  (0457605)

Refactoring

• Add forced yes and update UniprotID
  (b5ae58d)

• Add library install as well
  (c246b8b)

• Change to atomic command
  (5731223)

• Fix syntax issue
  (d765ea3)

• Improve notebook style
  (395975c)

• Make download jupyter compatible
  (be416af)

• Pipe yes
  (db5a8ce)

• Remove -qq issue
  (1385248)

• Remove potentially problematic quiet
  (e730e9c)

• Revert to debian non-interactive
  (73c0057)

• Shell dssp
  (7019339)

• Switch to uv install
  (3a3f6cf)

v2.0.5 (2025-04-28)

Bug Fixes

• Refactor DB utils and update examples
  (84abd4d)

This PR introduces several improvements to the handling of the alignment database and updates the
chainsaw.py example accordingly. Key Changes: Database Utilities (src/flatprot/utils/database.py):
Refactored DEFAULT_DB_DIR to use platformdirs for a standard, cross-platform data location
(rostlab/flatprot). Updated DEFAULT_DB_URL to point to the correct Zenodo archive
(alignment_db.zip). Added verify=False to the httpx client during download to mitigate potential
SSL certificate verification errors (includes a warning log). Improved the archive extraction
logic in download_database to: Extract to a temporary location. Specifically look for the
alignment_db folder within the archive. Move the contents of alignment_db to the final target
directory. Ignore other files/folders in the archive (like __MACOSX). Adjusted logging levels for
better clarity during download/extraction. Chainsaw Example (examples/chainsaw.py): Updated the
script to use the new flatprot.utils.database.ensure_database_available function to locate or
download the alignment database, removing hardcoded paths. Commented out Colab-specific shell
commands (!pip, !wget, etc.) to resolve linter errors and ensure the file is valid Python syntax.
Added the missing import for ensure_database_available. Motivation: To make the alignment database
download and storage more robust and platform-independent. To resolve issues related to SSL
verification and archive structure during database download. To ensure the example script utilizes
the centralized database handling logic. To fix linter errors in the example script.

Chores

• Remove CNAME
  (8ac9db4)

• Update connector color
  (979fe58)

v2.0.4 (2025-04-28)

Bug Fixes

• Documentation updates
  (9cd4af7)

v2.0.3 (2025-04-28)

Continuous Integration

• Simplify release config
  (0d929c3)

• Update mkdocs command
  (6cd2768)

v2.0.2 (2025-04-28)

Chores

• Generate example notebooks (#9,
  31ec311)

Automated generation of Jupyter notebooks from example Python scripts. Changes detected in
examples/*.py.

Co-authored-by: t03i t03i@users.noreply.github.com

Continuous Integration

• Add deps to docs-release
  (c4bfb08)

• Add labels permission
  (4fb5d23)

• Add repo checkout to finalize-release
  (41885a6)

• Update notebook pull request
  (d23e6b6)

• Update pull request permissions
  (c4ad0dc)

Documentation

• Update README
  (ee64954)

v2.0.1 (2025-04-22)

v2.0.0 (2025-04-22)

Bug Fixes

• Add - to allow for negative coords
  (f4df4a0)

• Add connection styles
  (771c228)

• Add opacity drawing
  (2d54351)

• Better checkpoint usage
  (a1f1f0c)

• Connection calculation
  (5a6b9ab)

• Dix dssp parsing
  (ed3fc37)

• Filter for target db now working
  (27b12c6)

• Import issues
  (563ba83)

• Improve error handling in alignment and transformation matrix
  (466356e)

• Enhanced error handling in the align_structure_rotation function by reintroducing specific
  handling for FlatProtError, ensuring consistent logging of error messages. - Added validation
  checks in the from_array and from_string methods of the TransformationMatrix class to ensure
  input arrays conform to expected dimensions, raising appropriate ValueError exceptions when
  necessary. - Updated docstrings for clarity and compliance with PEP257.

• Improve error handling in SVG rendering process
  (f1b310d)

• Wrapped the SVG rendering and saving logic in a try...except block to capture and log errors
  during the ...

v2.4.4

CHANGELOG

v2.1.0 (2025-04-30)

Chores

• Add runtime analysis
  (1847ea2)

Features

• Add runtime comparison script
  (36775ed)

Refactoring

• Ensure database path exists
  (283ecb0)

• Fix parameter
  (35c2621)

• Remove threads
  (c42db6d)

v2.0.6 (2025-04-29)

Bug Fixes

• Make database more robust for jupyter notebook
  (804a8ff)

Chores

• Add UniProt projection example tailed for Colab experience
  (#12,
  e287d01)

Summary This PR significantly improves the aesthetics and user experience of the

uniprot_projection.py example when viewed as a Google Colab notebook. The changes focus on visual
enhancements and interactive elements while maintaining the same functionality. ## Changes - Added
styled section headers with custom backgrounds and borders - Implemented interactive progress bars
for processing steps - Added color-coded status messages with appropriate icons (✅, ⚠️, ℹ️, ❌) -
Improved error and warning displays with formatted message boxes - Enhanced SVG display with
additional protein information card - Added visual feedback during long-running operations -
Improved configuration display with formatted tables - Added completion banner at the end of
execution - Added professional footer with attribution - Fixed cell structure for proper Colab
execution

Motivation The notebook acts as a demonstration tool for FlatProt functionality. These visual

enhancements make it more professional-looking and easier to follow for users exploring the tool
through Colab. The interactive elements also provide better feedback during execution.

Testing Tested in Google Colab environment to ensure all visual enhancements render correctly and

all functionality remains intact.

• Fix foldseek command test
  (b88a168)

Documentation

• Add better workflow description
  (8dc7a0a)

• Add PR rule to cursorrules
  (0457605)

Refactoring

• Add forced yes and update UniprotID
  (b5ae58d)

• Add library install as well
  (c246b8b)

• Change to atomic command
  (5731223)

• Fix syntax issue
  (d765ea3)

• Improve notebook style
  (395975c)

• Make download jupyter compatible
  (be416af)

• Pipe yes
  (db5a8ce)

• Remove -qq issue
  (1385248)

• Remove potentially problematic quiet
  (e730e9c)

• Revert to debian non-interactive
  (73c0057)

• Shell dssp
  (7019339)

• Switch to uv install
  (3a3f6cf)

v2.0.5 (2025-04-28)

Bug Fixes

• Refactor DB utils and update examples
  (84abd4d)

This PR introduces several improvements to the handling of the alignment database and updates the
chainsaw.py example accordingly. Key Changes: Database Utilities (src/flatprot/utils/database.py):
Refactored DEFAULT_DB_DIR to use platformdirs for a standard, cross-platform data location
(rostlab/flatprot). Updated DEFAULT_DB_URL to point to the correct Zenodo archive
(alignment_db.zip). Added verify=False to the httpx client during download to mitigate potential
SSL certificate verification errors (includes a warning log). Improved the archive extraction
logic in download_database to: Extract to a temporary location. Specifically look for the
alignment_db folder within the archive. Move the contents of alignment_db to the final target
directory. Ignore other files/folders in the archive (like __MACOSX). Adjusted logging levels for
better clarity during download/extraction. Chainsaw Example (examples/chainsaw.py): Updated the
script to use the new flatprot.utils.database.ensure_database_available function to locate or
download the alignment database, removing hardcoded paths. Commented out Colab-specific shell
commands (!pip, !wget, etc.) to resolve linter errors and ensure the file is valid Python syntax.
Added the missing import for ensure_database_available. Motivation: To make the alignment database
download and storage more robust and platform-independent. To resolve issues related to SSL
verification and archive structure during database download. To ensure the example script utilizes
the centralized database handling logic. To fix linter errors in the example script.

Chores

• Remove CNAME
  (8ac9db4)

• Update connector color
  (979fe58)

v2.0.4 (2025-04-28)

Bug Fixes

• Documentation updates
  (9cd4af7)

v2.0.3 (2025-04-28)

Continuous Integration

• Simplify release config
  (0d929c3)

• Update mkdocs command
  (6cd2768)

v2.0.2 (2025-04-28)

Chores

• Generate example notebooks (#9,
  31ec311)

Automated generation of Jupyter notebooks from example Python scripts. Changes detected in
examples/*.py.

Co-authored-by: t03i t03i@users.noreply.github.com

Continuous Integration

• Add deps to docs-release
  (c4bfb08)

• Add labels permission
  (4fb5d23)

• Add repo checkout to finalize-release
  (41885a6)

• Update notebook pull request
  (d23e6b6)

• Update pull request permissions
  (c4ad0dc)

Documentation

• Update README
  (ee64954)

v2.0.1 (2025-04-22)

v2.0.0 (2025-04-22)

Bug Fixes

• Add - to allow for negative coords
  (f4df4a0)

• Add connection styles
  (771c228)

• Add opacity drawing
  (2d54351)

• Better checkpoint usage
  (a1f1f0c)

• Connection calculation
  (5a6b9ab)

• Dix dssp parsing
  (ed3fc37)

• Filter for target db now working
  (27b12c6)

• Import issues
  (563ba83)

• Improve error handling in alignment and transformation matrix
  (466356e)

• Enhanced error handling in the align_structure_rotation function by reintroducing specific
  handling for FlatProtError, ensuring consistent logging of error messages. - Added validation
  checks in the from_array and from_string methods of the TransformationMatrix class to ensure
  input arrays conform to expected dimensions, raising appropriate ValueError exceptions when
  necessary. - Updated docstrings for clarity and compliance with PEP257.

• Improve error handling in SVG rendering process
  (f1b310d)

• Wrapped the SVG rendering and saving logic in a try...except block to capture and log errors
  during the ...

v2.4.3

CHANGELOG

v2.1.0 (2025-04-30)

Chores

• Add runtime analysis
  (1847ea2)

Features

• Add runtime comparison script
  (36775ed)

Refactoring

• Ensure database path exists
  (283ecb0)

• Fix parameter
  (35c2621)

• Remove threads
  (c42db6d)

v2.0.6 (2025-04-29)

Bug Fixes

• Make database more robust for jupyter notebook
  (804a8ff)

Chores

• Add UniProt projection example tailed for Colab experience
  (#12,
  e287d01)

Summary This PR significantly improves the aesthetics and user experience of the

uniprot_projection.py example when viewed as a Google Colab notebook. The changes focus on visual
enhancements and interactive elements while maintaining the same functionality. ## Changes - Added
styled section headers with custom backgrounds and borders - Implemented interactive progress bars
for processing steps - Added color-coded status messages with appropriate icons (✅, ⚠️, ℹ️, ❌) -
Improved error and warning displays with formatted message boxes - Enhanced SVG display with
additional protein information card - Added visual feedback during long-running operations -
Improved configuration display with formatted tables - Added completion banner at the end of
execution - Added professional footer with attribution - Fixed cell structure for proper Colab
execution

Motivation The notebook acts as a demonstration tool for FlatProt functionality. These visual

enhancements make it more professional-looking and easier to follow for users exploring the tool
through Colab. The interactive elements also provide better feedback during execution.

Testing Tested in Google Colab environment to ensure all visual enhancements render correctly and

all functionality remains intact.

• Fix foldseek command test
  (b88a168)

Documentation

• Add better workflow description
  (8dc7a0a)

• Add PR rule to cursorrules
  (0457605)

Refactoring

• Add forced yes and update UniprotID
  (b5ae58d)

• Add library install as well
  (c246b8b)

• Change to atomic command
  (5731223)

• Fix syntax issue
  (d765ea3)

• Improve notebook style
  (395975c)

• Make download jupyter compatible
  (be416af)

• Pipe yes
  (db5a8ce)

• Remove -qq issue
  (1385248)

• Remove potentially problematic quiet
  (e730e9c)

• Revert to debian non-interactive
  (73c0057)

• Shell dssp
  (7019339)

• Switch to uv install
  (3a3f6cf)

v2.0.5 (2025-04-28)

Bug Fixes

• Refactor DB utils and update examples
  (84abd4d)

This PR introduces several improvements to the handling of the alignment database and updates the
chainsaw.py example accordingly. Key Changes: Database Utilities (src/flatprot/utils/database.py):
Refactored DEFAULT_DB_DIR to use platformdirs for a standard, cross-platform data location
(rostlab/flatprot). Updated DEFAULT_DB_URL to point to the correct Zenodo archive
(alignment_db.zip). Added verify=False to the httpx client during download to mitigate potential
SSL certificate verification errors (includes a warning log). Improved the archive extraction
logic in download_database to: Extract to a temporary location. Specifically look for the
alignment_db folder within the archive. Move the contents of alignment_db to the final target
directory. Ignore other files/folders in the archive (like __MACOSX). Adjusted logging levels for
better clarity during download/extraction. Chainsaw Example (examples/chainsaw.py): Updated the
script to use the new flatprot.utils.database.ensure_database_available function to locate or
download the alignment database, removing hardcoded paths. Commented out Colab-specific shell
commands (!pip, !wget, etc.) to resolve linter errors and ensure the file is valid Python syntax.
Added the missing import for ensure_database_available. Motivation: To make the alignment database
download and storage more robust and platform-independent. To resolve issues related to SSL
verification and archive structure during database download. To ensure the example script utilizes
the centralized database handling logic. To fix linter errors in the example script.

Chores

• Remove CNAME
  (8ac9db4)

• Update connector color
  (979fe58)

v2.0.4 (2025-04-28)

Bug Fixes

• Documentation updates
  (9cd4af7)

v2.0.3 (2025-04-28)

Continuous Integration

• Simplify release config
  (0d929c3)

• Update mkdocs command
  (6cd2768)

v2.0.2 (2025-04-28)

Chores

• Generate example notebooks (#9,
  31ec311)

Automated generation of Jupyter notebooks from example Python scripts. Changes detected in
examples/*.py.

Co-authored-by: t03i t03i@users.noreply.github.com

Continuous Integration

• Add deps to docs-release
  (c4bfb08)

• Add labels permission
  (4fb5d23)

• Add repo checkout to finalize-release
  (41885a6)

• Update notebook pull request
  (d23e6b6)

• Update pull request permissions
  (c4ad0dc)

Documentation

• Update README
  (ee64954)

v2.0.1 (2025-04-22)

v2.0.0 (2025-04-22)

Bug Fixes

• Add - to allow for negative coords
  (f4df4a0)

• Add connection styles
  (771c228)

• Add opacity drawing
  (2d54351)

• Better checkpoint usage
  (a1f1f0c)

• Connection calculation
  (5a6b9ab)

• Dix dssp parsing
  (ed3fc37)

• Filter for target db now working
  (27b12c6)

• Import issues
  (563ba83)

• Improve error handling in alignment and transformation matrix
  (466356e)

• Enhanced error handling in the align_structure_rotation function by reintroducing specific
  handling for FlatProtError, ensuring consistent logging of error messages. - Added validation
  checks in the from_array and from_string methods of the TransformationMatrix class to ensure
  input arrays conform to expected dimensions, raising appropriate ValueError exceptions when
  necessary. - Updated docstrings for clarity and compliance with PEP257.

• Improve error handling in SVG rendering process
  (f1b310d)

• Wrapped the SVG rendering and saving logic in a try...except block to capture and log errors
  during the ...

v2.4.2

CHANGELOG

v2.1.0 (2025-04-30)

Chores

• Add runtime analysis
  (1847ea2)

Features

• Add runtime comparison script
  (36775ed)

Refactoring

• Ensure database path exists
  (283ecb0)

• Fix parameter
  (35c2621)

• Remove threads
  (c42db6d)

v2.0.6 (2025-04-29)

Bug Fixes

• Make database more robust for jupyter notebook
  (804a8ff)

Chores

• Add UniProt projection example tailed for Colab experience
  (#12,
  e287d01)

Summary This PR significantly improves the aesthetics and user experience of the

uniprot_projection.py example when viewed as a Google Colab notebook. The changes focus on visual
enhancements and interactive elements while maintaining the same functionality. ## Changes - Added
styled section headers with custom backgrounds and borders - Implemented interactive progress bars
for processing steps - Added color-coded status messages with appropriate icons (✅, ⚠️, ℹ️, ❌) -
Improved error and warning displays with formatted message boxes - Enhanced SVG display with
additional protein information card - Added visual feedback during long-running operations -
Improved configuration display with formatted tables - Added completion banner at the end of
execution - Added professional footer with attribution - Fixed cell structure for proper Colab
execution

Motivation The notebook acts as a demonstration tool for FlatProt functionality. These visual

enhancements make it more professional-looking and easier to follow for users exploring the tool
through Colab. The interactive elements also provide better feedback during execution.

Testing Tested in Google Colab environment to ensure all visual enhancements render correctly and

all functionality remains intact.

• Fix foldseek command test
  (b88a168)

Documentation

• Add better workflow description
  (8dc7a0a)

• Add PR rule to cursorrules
  (0457605)

Refactoring

• Add forced yes and update UniprotID
  (b5ae58d)

• Add library install as well
  (c246b8b)

• Change to atomic command
  (5731223)

• Fix syntax issue
  (d765ea3)

• Improve notebook style
  (395975c)

• Make download jupyter compatible
  (be416af)

• Pipe yes
  (db5a8ce)

• Remove -qq issue
  (1385248)

• Remove potentially problematic quiet
  (e730e9c)

• Revert to debian non-interactive
  (73c0057)

• Shell dssp
  (7019339)

• Switch to uv install
  (3a3f6cf)

v2.0.5 (2025-04-28)

Bug Fixes

• Refactor DB utils and update examples
  (84abd4d)

This PR introduces several improvements to the handling of the alignment database and updates the
chainsaw.py example accordingly. Key Changes: Database Utilities (src/flatprot/utils/database.py):
Refactored DEFAULT_DB_DIR to use platformdirs for a standard, cross-platform data location
(rostlab/flatprot). Updated DEFAULT_DB_URL to point to the correct Zenodo archive
(alignment_db.zip). Added verify=False to the httpx client during download to mitigate potential
SSL certificate verification errors (includes a warning log). Improved the archive extraction
logic in download_database to: Extract to a temporary location. Specifically look for the
alignment_db folder within the archive. Move the contents of alignment_db to the final target
directory. Ignore other files/folders in the archive (like __MACOSX). Adjusted logging levels for
better clarity during download/extraction. Chainsaw Example (examples/chainsaw.py): Updated the
script to use the new flatprot.utils.database.ensure_database_available function to locate or
download the alignment database, removing hardcoded paths. Commented out Colab-specific shell
commands (!pip, !wget, etc.) to resolve linter errors and ensure the file is valid Python syntax.
Added the missing import for ensure_database_available. Motivation: To make the alignment database
download and storage more robust and platform-independent. To resolve issues related to SSL
verification and archive structure during database download. To ensure the example script utilizes
the centralized database handling logic. To fix linter errors in the example script.

Chores

• Remove CNAME
  (8ac9db4)

• Update connector color
  (979fe58)

v2.0.4 (2025-04-28)

Bug Fixes

• Documentation updates
  (9cd4af7)

v2.0.3 (2025-04-28)

Continuous Integration

• Simplify release config
  (0d929c3)

• Update mkdocs command
  (6cd2768)

v2.0.2 (2025-04-28)

Chores

• Generate example notebooks (#9,
  31ec311)

Automated generation of Jupyter notebooks from example Python scripts. Changes detected in
examples/*.py.

Co-authored-by: t03i t03i@users.noreply.github.com

Continuous Integration

• Add deps to docs-release
  (c4bfb08)

• Add labels permission
  (4fb5d23)

• Add repo checkout to finalize-release
  (41885a6)

• Update notebook pull request
  (d23e6b6)

• Update pull request permissions
  (c4ad0dc)

Documentation

• Update README
  (ee64954)

v2.0.1 (2025-04-22)

v2.0.0 (2025-04-22)

Bug Fixes

• Add - to allow for negative coords
  (f4df4a0)

• Add connection styles
  (771c228)

• Add opacity drawing
  (2d54351)

• Better checkpoint usage
  (a1f1f0c)

• Connection calculation
  (5a6b9ab)

• Dix dssp parsing
  (ed3fc37)

• Filter for target db now working
  (27b12c6)

• Import issues
  (563ba83)

• Improve error handling in alignment and transformation matrix
  (466356e)

• Enhanced error handling in the align_structure_rotation function by reintroducing specific
  handling for FlatProtError, ensuring consistent logging of error messages. - Added validation
  checks in the from_array and from_string methods of the TransformationMatrix class to ensure
  input arrays conform to expected dimensions, raising appropriate ValueError exceptions when
  necessary. - Updated docstrings for clarity and compliance with PEP257.

• Improve error handling in SVG rendering process
  (f1b310d)

• Wrapped the SVG rendering and saving logic in a try...except block to capture and log errors
  during the ...

v2.4.1

CHANGELOG

v2.1.0 (2025-04-30)

Chores

• Add runtime analysis
  (1847ea2)

Features

• Add runtime comparison script
  (36775ed)

Refactoring

• Ensure database path exists
  (283ecb0)

• Fix parameter
  (35c2621)

• Remove threads
  (c42db6d)

v2.0.6 (2025-04-29)

Bug Fixes

• Make database more robust for jupyter notebook
  (804a8ff)

Chores

• Add UniProt projection example tailed for Colab experience
  (#12,
  e287d01)

Summary This PR significantly improves the aesthetics and user experience of the

uniprot_projection.py example when viewed as a Google Colab notebook. The changes focus on visual
enhancements and interactive elements while maintaining the same functionality. ## Changes - Added
styled section headers with custom backgrounds and borders - Implemented interactive progress bars
for processing steps - Added color-coded status messages with appropriate icons (✅, ⚠️, ℹ️, ❌) -
Improved error and warning displays with formatted message boxes - Enhanced SVG display with
additional protein information card - Added visual feedback during long-running operations -
Improved configuration display with formatted tables - Added completion banner at the end of
execution - Added professional footer with attribution - Fixed cell structure for proper Colab
execution

Motivation The notebook acts as a demonstration tool for FlatProt functionality. These visual

enhancements make it more professional-looking and easier to follow for users exploring the tool
through Colab. The interactive elements also provide better feedback during execution.

Testing Tested in Google Colab environment to ensure all visual enhancements render correctly and

all functionality remains intact.

• Fix foldseek command test
  (b88a168)

Documentation

• Add better workflow description
  (8dc7a0a)

• Add PR rule to cursorrules
  (0457605)

Refactoring

• Add forced yes and update UniprotID
  (b5ae58d)

• Add library install as well
  (c246b8b)

• Change to atomic command
  (5731223)

• Fix syntax issue
  (d765ea3)

• Improve notebook style
  (395975c)

• Make download jupyter compatible
  (be416af)

• Pipe yes
  (db5a8ce)

• Remove -qq issue
  (1385248)

• Remove potentially problematic quiet
  (e730e9c)

• Revert to debian non-interactive
  (73c0057)

• Shell dssp
  (7019339)

• Switch to uv install
  (3a3f6cf)

v2.0.5 (2025-04-28)

Bug Fixes

• Refactor DB utils and update examples
  (84abd4d)

This PR introduces several improvements to the handling of the alignment database and updates the
chainsaw.py example accordingly. Key Changes: Database Utilities (src/flatprot/utils/database.py):
Refactored DEFAULT_DB_DIR to use platformdirs for a standard, cross-platform data location
(rostlab/flatprot). Updated DEFAULT_DB_URL to point to the correct Zenodo archive
(alignment_db.zip). Added verify=False to the httpx client during download to mitigate potential
SSL certificate verification errors (includes a warning log). Improved the archive extraction
logic in download_database to: Extract to a temporary location. Specifically look for the
alignment_db folder within the archive. Move the contents of alignment_db to the final target
directory. Ignore other files/folders in the archive (like __MACOSX). Adjusted logging levels for
better clarity during download/extraction. Chainsaw Example (examples/chainsaw.py): Updated the
script to use the new flatprot.utils.database.ensure_database_available function to locate or
download the alignment database, removing hardcoded paths. Commented out Colab-specific shell
commands (!pip, !wget, etc.) to resolve linter errors and ensure the file is valid Python syntax.
Added the missing import for ensure_database_available. Motivation: To make the alignment database
download and storage more robust and platform-independent. To resolve issues related to SSL
verification and archive structure during database download. To ensure the example script utilizes
the centralized database handling logic. To fix linter errors in the example script.

Chores

• Remove CNAME
  (8ac9db4)

• Update connector color
  (979fe58)

v2.0.4 (2025-04-28)

Bug Fixes

• Documentation updates
  (9cd4af7)

v2.0.3 (2025-04-28)

Continuous Integration

• Simplify release config
  (0d929c3)

• Update mkdocs command
  (6cd2768)

v2.0.2 (2025-04-28)

Chores

• Generate example notebooks (#9,
  31ec311)

Automated generation of Jupyter notebooks from example Python scripts. Changes detected in
examples/*.py.

Co-authored-by: t03i t03i@users.noreply.github.com

Continuous Integration

• Add deps to docs-release
  (c4bfb08)

• Add labels permission
  (4fb5d23)

• Add repo checkout to finalize-release
  (41885a6)

• Update notebook pull request
  (d23e6b6)

• Update pull request permissions
  (c4ad0dc)

Documentation

• Update README
  (ee64954)

v2.0.1 (2025-04-22)

v2.0.0 (2025-04-22)

Bug Fixes

• Add - to allow for negative coords
  (f4df4a0)

• Add connection styles
  (771c228)

• Add opacity drawing
  (2d54351)

• Better checkpoint usage
  (a1f1f0c)

• Connection calculation
  (5a6b9ab)

• Dix dssp parsing
  (ed3fc37)

• Filter for target db now working
  (27b12c6)

• Import issues
  (563ba83)

• Improve error handling in alignment and transformation matrix
  (466356e)

• Enhanced error handling in the align_structure_rotation function by reintroducing specific
  handling for FlatProtError, ensuring consistent logging of error messages. - Added validation
  checks in the from_array and from_string methods of the TransformationMatrix class to ensure
  input arrays conform to expected dimensions, raising appropriate ValueError exceptions when
  necessary. - Updated docstrings for clarity and compliance with PEP257.

• Improve error handling in SVG rendering process
  (f1b310d)

• Wrapped the SVG rendering and saving logic in a try...except block to capture and log errors
  during the ...

v2.4.0

CHANGELOG

v2.1.0 (2025-04-30)

Chores

• Add runtime analysis
  (1847ea2)

Features

• Add runtime comparison script
  (36775ed)

Refactoring

• Ensure database path exists
  (283ecb0)

• Fix parameter
  (35c2621)

• Remove threads
  (c42db6d)

v2.0.6 (2025-04-29)

Bug Fixes

• Make database more robust for jupyter notebook
  (804a8ff)

Chores

• Add UniProt projection example tailed for Colab experience
  (#12,
  e287d01)

Summary This PR significantly improves the aesthetics and user experience of the

uniprot_projection.py example when viewed as a Google Colab notebook. The changes focus on visual
enhancements and interactive elements while maintaining the same functionality. ## Changes - Added
styled section headers with custom backgrounds and borders - Implemented interactive progress bars
for processing steps - Added color-coded status messages with appropriate icons (✅, ⚠️, ℹ️, ❌) -
Improved error and warning displays with formatted message boxes - Enhanced SVG display with
additional protein information card - Added visual feedback during long-running operations -
Improved configuration display with formatted tables - Added completion banner at the end of
execution - Added professional footer with attribution - Fixed cell structure for proper Colab
execution

Motivation The notebook acts as a demonstration tool for FlatProt functionality. These visual

enhancements make it more professional-looking and easier to follow for users exploring the tool
through Colab. The interactive elements also provide better feedback during execution.

Testing Tested in Google Colab environment to ensure all visual enhancements render correctly and

all functionality remains intact.

• Fix foldseek command test
  (b88a168)

Documentation

• Add better workflow description
  (8dc7a0a)

• Add PR rule to cursorrules
  (0457605)

Refactoring

• Add forced yes and update UniprotID
  (b5ae58d)

• Add library install as well
  (c246b8b)

• Change to atomic command
  (5731223)

• Fix syntax issue
  (d765ea3)

• Improve notebook style
  (395975c)

• Make download jupyter compatible
  (be416af)

• Pipe yes
  (db5a8ce)

• Remove -qq issue
  (1385248)

• Remove potentially problematic quiet
  (e730e9c)

• Revert to debian non-interactive
  (73c0057)

• Shell dssp
  (7019339)

• Switch to uv install
  (3a3f6cf)

v2.0.5 (2025-04-28)

Bug Fixes

• Refactor DB utils and update examples
  (84abd4d)

This PR introduces several improvements to the handling of the alignment database and updates the
chainsaw.py example accordingly. Key Changes: Database Utilities (src/flatprot/utils/database.py):
Refactored DEFAULT_DB_DIR to use platformdirs for a standard, cross-platform data location
(rostlab/flatprot). Updated DEFAULT_DB_URL to point to the correct Zenodo archive
(alignment_db.zip). Added verify=False to the httpx client during download to mitigate potential
SSL certificate verification errors (includes a warning log). Improved the archive extraction
logic in download_database to: Extract to a temporary location. Specifically look for the
alignment_db folder within the archive. Move the contents of alignment_db to the final target
directory. Ignore other files/folders in the archive (like __MACOSX). Adjusted logging levels for
better clarity during download/extraction. Chainsaw Example (examples/chainsaw.py): Updated the
script to use the new flatprot.utils.database.ensure_database_available function to locate or
download the alignment database, removing hardcoded paths. Commented out Colab-specific shell
commands (!pip, !wget, etc.) to resolve linter errors and ensure the file is valid Python syntax.
Added the missing import for ensure_database_available. Motivation: To make the alignment database
download and storage more robust and platform-independent. To resolve issues related to SSL
verification and archive structure during database download. To ensure the example script utilizes
the centralized database handling logic. To fix linter errors in the example script.

Chores

• Remove CNAME
  (8ac9db4)

• Update connector color
  (979fe58)

v2.0.4 (2025-04-28)

Bug Fixes

• Documentation updates
  (9cd4af7)

v2.0.3 (2025-04-28)

Continuous Integration

• Simplify release config
  (0d929c3)

• Update mkdocs command
  (6cd2768)

v2.0.2 (2025-04-28)

Chores

• Generate example notebooks (#9,
  31ec311)

Automated generation of Jupyter notebooks from example Python scripts. Changes detected in
examples/*.py.

Co-authored-by: t03i t03i@users.noreply.github.com

Continuous Integration

• Add deps to docs-release
  (c4bfb08)

• Add labels permission
  (4fb5d23)

• Add repo checkout to finalize-release
  (41885a6)

• Update notebook pull request
  (d23e6b6)

• Update pull request permissions
  (c4ad0dc)

Documentation

• Update README
  (ee64954)

v2.0.1 (2025-04-22)

v2.0.0 (2025-04-22)

Bug Fixes

• Add - to allow for negative coords
  (f4df4a0)

• Add connection styles
  (771c228)

• Add opacity drawing
  (2d54351)

• Better checkpoint usage
  (a1f1f0c)

• Connection calculation
  (5a6b9ab)

• Dix dssp parsing
  (ed3fc37)

• Filter for target db now working
  (27b12c6)

• Import issues
  (563ba83)

• Improve error handling in alignment and transformation matrix
  (466356e)

• Enhanced error handling in the align_structure_rotation function by reintroducing specific
  handling for FlatProtError, ensuring consistent logging of error messages. - Added validation
  checks in the from_array and from_string methods of the TransformationMatrix class to ensure
  input arrays conform to expected dimensions, raising appropriate ValueError exceptions when
  necessary. - Updated docstrings for clarity and compliance with PEP257.

• Improve error handling in SVG rendering process
  (f1b310d)

• Wrapped the SVG rendering and saving logic in a try...except block to capture and log errors
  during the ...