v1.1.0: Post-review release

Release date: 04.04.2022.

Added:

• Implemented depth analysis workflow.
• Implemented simple scatter plot visualization. Added precached depth data sets.
• Implemented multiple new things to support the new case study.
• Updated cluster visualization with temporal information

Changed:

• Changed some function names after upgrading Streamlit to a new version.
• Changed the way Streamlit is installed with a Docker file. Now it uses pip instead of conda.
• Removed triple dot menu above each visualization. A new saving method is implemented. Changed visualization download functionality from built-in to the in-house method.
• Changed the name of Two features scatter-plot to Two features plot, to better reflect the resulting visualization.
• Changed time heatmap default color scheme for sequential data.
• Compressed Example 2 data set for better performance.

Fixed:

• Fixed a bug that caused FileNotFoundError when the user uploaded an archived data set. Fixed multiple regressions.
• Fixed a bug present in the arrow serialization engine. Returned to legacy serialization on Streamlit.
• Fixed a bug that happens when dataframe has a column of FLoat64 type and a user wants to save a visualization of that dataframe.
• Fixed a bug with the session state that cause the front-end to hang.
• Fixed some things with pandas.describe() so that there are no more warnings.

Security:

• Upgraded Streamlit to version 1.5.1

Detailed:

• efd333f (HEAD -> master, origin/master, origin/HEAD) Changed: Updated README.md with citations and images.
• 458fce5 Changed: Updated README.md with citations and images.
• c1819c3 Changed: Updated README.md with citations and images.
• 9b611b0 Merge pull request #3 from bgruening/patch-1
  |\
  | * 601669e add bibtex
• | 42817d7 Changed: Updated CITATION.cff
  |/
• 92828b9 (tag: v1.0.6) Changed: Compressed Example 2 data set for better performance.
• 58aa838 Updated: Updated streamlit library.
• 19f7f16 Changed: Updated some sections of the UI after the second revision of the tool.
• a8ac63c Changed: Updated README.md
• af100e5 (tag: v1.0.5) Fixed: Fixed a bug that appeared with version bump.
• b27a314 Updated: Updated libraries to up-to-date versions.
• dd4cafb Updated: Updated libraries to up-to-date versions.
• a697ec7 Changed: Changed info text to better reflect the original data set.
• b54ae2c Changed: Changed the placement of the legend in the Time heatmap visualization from upper right to bottom.
• 25a65dd Changed: Added small visual changes where needed. Added: Added important file extension check for archived data sets. Added title to the whisker plot. Fixed: Some small bugs were fixed.
• d1afa6d Improved: Changed some example 2 parameters so that we have a consistent UI with the rest of MOVIS.
• dfce970 Added: Updated Example 1 with new data from the case study.
• 6f1c689 Improved: Added more options to Time Heatmap chart.
• cb0af84 Improved: Added more options to Time Heatmap chart.
• 66baa97 Changed: Changed preprocessed metabolomics data set to the other one available from the example 1 data set. Changed the order of omics appearance to reflect the manuscript order.
• 58b012b Improved: Updated Feature through time tooltip with color channel information.
• 160f2b1 Changed: Removed calculation of additional physico-chemical properties for metaproteomics data set for the case study.
• 051ecc3 Improved: Changed time heatmap y axis to show year and month.
• b4b38e7 Added: Added more preselected values to support case study. Completed the whole preselection process.
• 584fa89 Added: Added more preselected values to support case study. Metaproteomics clustering method is now preselected, along with the appropriate visualizations.
• 5248fd0 Added: Added more preselected values to support case study. Metaproteomics additional properties FASTA data is now preselected.
• 155b7de Added: Added more default options to support the upcoming case study. Changed: Changed data type in Time Heatmap from temporal to ordinal in order to have centered ticks.
• 380e160 Added: Started preselecting visualization and certain visualization parameters for the case study. Added multiple supporting functions for the case study.
• 4bfff06 Added: Started preselecting visualization and certain visualization parameters for the case study. Added multiple supporting functions for the case study.
• aa111e3 Changed: Changed some key_suffix parsing templates.
• 61bac1c Changed: Updated cluster visualization with temporal information. Fixed: Fixed some clustering-related bugs.
• 5ce49b8 Changed: Changed time heatmap default color scheme for sequential data.
• ed4d683 Changed: Changed time heatmap default color scheme for sequential data.
• f27d2a4 Added: Implemented case study default omics. Those omics will be used to tell a story.
• fb6bf76 Added: Implemented case study default omics. Those omics will be used to tell a story.
• a9d948e Added: Implemented multiple new things to support new case study. Fixed: Fixed some minor bugs.
• bbe054c Changed: Changed some text. Started creating case study layout.
• 998399f Added: Added precalculated metabolomics/physico-chemical data set for use case page.
• a99231b Added: Cached new transcriptomics data set for the Example 1. Added data set limit check, since we cannot visualize dataframes that are greater than 50MB or 15000 rows.
• 212e2c5 Changed: Renamed use case to case study.
• ad6c263 Changed: Time heatmap now has datetime on both axes. Other feature is encoded with color. Fixed: Fixed some things with pandas.describe() so that there are no more warnings.
• 8336a31 Changed: Time heatmap now has datetime on both axes. Other feature is encoded with color. Fixed: Fixed some things with pandas.describe() so that there are no more warnings.
• 0033817 Added: Implemented some features for the use case page.
• 7b95637 Added: Implemented simple scatter plot visualization. Added precached depth data sets.
• a00694f Added: Implemented fully depth analysis.
• d0233ba Added: Implemented depth analysis workflow.
• 2132e77 Added: Added whisker chart visualization to support new data set.
• f660627 Changed: Updated new data set names according to the documentation standard.
• 5d163b8 Added: Added new visualization (Time heatmap) type and made it available.
• 8f03842 Added: Added new visualization (Time heatmap) type and made it available.
• 67087fb Added: Implemented template functions that work with new Depth-of-coverage data sets.
• f76285a Added: Updated Example 1 script for new data.
• c671611 Added: Added paths for new Example 1 data.
• e010cbe Added: Uploaded metagenomics and metatranscriptomics depth data for Example 1.
• 7c3fb96 Changed: Adapted code according to FLAKE8 linting.
• 9637450 Added: Implemented new visualization. Still in testing phase.
• 8211b38 Fixed: Fixed a bug with session state that cause the front-end to hang. Changed: Changed the name of Two features scatter-plot to Two features plot, to better reflect the resuting visualization.
• 3673c44 Fixed: Fixed a bug with session state that cause the front-end to hang. Changed: Changed the name of Two features scatter-plot to Two features plot, to better reflect the resuting visualization.
• 50d5e07 Add: Recached examples.
• 80fdb4f Changed: Updated README with new abstract.
• 12f18ee Add: Recached examples. Fix: Fixed small bugs.
• e193559 Changed: Changed omic names for the Example 1 from 'Omic' to 'Metaomic' to better reflect the underlying data sets.
• 0b2be89 Changed: Changed omic names for the Example 1 from 'Omic' to 'Metaomic' to better reflect the underlying data sets.
• 62911fc Changed: Changed omic names for the Example 1 from 'Omic' to 'Metaomic' to better reflect the underlying data sets.
• ec51442 Improved: Updated column names for the embedded data sets.
• 32f3a4d Changed: Changed an image export method. Added multiple new functions for this functionality. Fix: Fixed a bug that happens when dataframe has a column of FLoat64 type and a user wants to save a visualization of that dataframe.
• fe21516 Changed: Changed image export libraries.
• 57ff25e Improved: Updated README with new packages.
• 96314ad Improved: Changed visualization download functionality from built-in to in-house method. Visualizations will now be downloaded using a button.
• 3419c61 Removed: Removed triple dot menu above each visualization. New saving method will soon be implemented.
• b1d2441 Changed: Data format information is now more visible and presented using expanders.
• ac146e2 Removed: Removed expanders that seperated exploration and visualization part. Expanders will now be used for showing additional text information.
• 011d22e Fix: Fixed a bug present in the arrow serialization engine. Returned to legacy serialization on streamlit. Improv: Changed some text description.
• b63e9cf Fix: Fixed a bug that caused FileNotFoundError when user uploaded an archived data set. Fixed multiple regressions.
• faf6a3b Improv: Improved certain table descriptions.
• 19e67da Add: Updated Dockerfile with python-levenshtein package. This package is needed for gensim to work properly.
• 0c6df0d Add: Updated Dockerfile with python-levenshtein package. This package is needed for gensim to work properly.
• 1ee8f4c feat (visualization): Implemented vertical ruler with a tooltip for the Feature through time visualization.

v1.0.4: QoL fixes

VERSION 1.0.4

Release date: 13.10.2021.

Changed:

1. Changed some function names after upgrading Streamlit to a new version.
2. Changed the way Streamlit is installed with a Docker file. Now it uses pip instead of conda.

Removed:

1. Removed interactive elements of specific charts.

Fixed:

1. Fixed a critical bug that enabled users to remove cached data sets.
2. Fixed a bug that caused showing the duplicate titles for every plot in the scatter matrix chart.
3. Fixed a bug with pandas describe function.

Security:

1. Upgraded Streamlit to version 1.0.0

v1.0.3: QoL fixes

VERSION 1.0.3
Release date: 15.09.2021

[Changed]: Updated README.

[Removed]: KEGG annotation files for example 1.

[Fixed]: A bug that caused showing wrong folder structure for genomics data of example 1.

v1.0.2: Server-related fixes

This release fixes some bugs we encountered after deploying MOVIS to a server. We fixed some bugs related to file size limits.

v1.0.1: Docker adaptation

This release fixes some bugs for DockerHub deployment.

v1.0.0: First Public Release

The initial release of MOVIS for paper publication.