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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,167 +1,39 @@ | ||
| .. | ||
| Copyright (c) 2015, 2016 Florian Wagner | ||
| Copyright (c) 2017 Florian Wagner | ||
| This file is part of GO-PCA. | ||
| GO-PCA is free software: you can redistribute it and/or modify | ||
| it under the terms of the GNU General Public License, Version 3, | ||
| it under the terms of the GNU Affero General Public License, Version 3, | ||
| as published by the Free Software Foundation. | ||
| This program is distributed in the hope that it will be useful, | ||
| but WITHOUT ANY WARRANTY; without even the implied warranty of | ||
| MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the | ||
| GNU General Public License for more details. | ||
| GNU Affero General Public License for more details. | ||
| You should have received a copy of the GNU General Public License | ||
| You should have received a copy of the GNU Affero General Public License | ||
| along with this program. If not, see <http://www.gnu.org/licenses/>. | ||
|
|
||
| Changelog | ||
| ========= | ||
|
|
||
| Version 2.1.0 (2016-08-28) | ||
| Version 0.2.3 (2017-03-08) | ||
| -------------------------- | ||
|
|
||
| - Improved algorithm for generating signatures based on significantly enriched | ||
| gene sets, and introduced a new parameter, ``sig_min_genes`` to specify the | ||
| minimum number of genes in each signature. Effectively, this makes gene set | ||
| enrichment analysis and signature generation more independent of each other, | ||
| and results in more coherent signatures (i.e., genes in a signature should | ||
| have more similar expression patterns with the new algorithm). | ||
|
|
||
| - Improved the "Installing GO-PCA" section of the documentation. The section | ||
| now includes accurate instructions for Windows and Mac OS X. | ||
|
|
||
| - Reduced the verbosity of GO-PCA output. The old verbosity can be restored | ||
| by passing ``verbose=True`` to GO-PCA, or by running the ``go-pca.py`` script | ||
| with the ``-v`` option. | ||
|
|
||
| - Changed data structure used for representing signature matrices | ||
| (`GOPCASignatureMatrix` now inherits from `genometools.expression.ExpMatrix`). | ||
|
|
||
| - Added simplified functions for plotting heatmaps of signature matrices | ||
| and signature genes to the Python API: `GOPCASignatureMatrix.get_figure()` | ||
| and `GOPCASignature.get_figure()`. | ||
|
|
||
| 2.1.1 (2016-09-04) | ||
| ~~~~~~~~~~~~~~~~~~ | ||
|
|
||
| - Travis deploy step now generates and uploads wheels. | ||
| - Fixed bug in `GOPCASignatureMatrix.filter_collection_signatures()`. | ||
|
|
||
| 2.1.2 (2016-09-04) | ||
| ~~~~~~~~~~~~~~~~~~ | ||
|
|
||
| - Changed genometools dependency to version 2.0.2. | ||
|
|
||
| 2.1.3 (2016-09-04) | ||
| ~~~~~~~~~~~~~~~~~~ | ||
|
|
||
| - Renamed `GOPCA.simple_init()` to `simple_setup()`. | ||
|
|
||
| 2.1.4 (2016-10-06) | ||
| ------------------ | ||
|
|
||
| - Modified `GOPCASignature.get_figure()` call signature. | ||
|
|
||
| Version 2.0.0 (2016-08-01) | ||
| -------------------------- | ||
|
|
||
| - Generalized the API to support multiple "configurations" as input. Each | ||
| configuration (`GOPCAConfig`) consists of a set of GO-PCA parameters | ||
| (`GOPCAParams`), a list of gene sets | ||
| (`genometools.basic.GeneSetCollection`), and, optionally, a gene ontology | ||
| (`genometools.ontology.GeneOntology`). GO-PCA is performed independently | ||
| for each configuration, and the signatures generated are merged into a | ||
| single signature matrix. The old way of configuring GO-PCA is available as | ||
| `GOPCA.simple_setup()`. | ||
|
|
||
| Version 2.0.1 (2016-08-16) | ||
| ~~~~~~~~~~~~~~~~~~~~~~~~~~ | ||
| - Some bugfixes | ||
|
|
||
| Version 1.2.0 (2016-07-26) | ||
| -------------------------- | ||
|
|
||
| - Full Python 3.5 support (on top of Python 2.7) | ||
| - New Python API for running GO-PCA, accessing results and generating figures | ||
| - Integrated code with genometools 2.0 | ||
| - Cleaned up code | ||
| - Added tests (using py.test) | ||
| - Switched to plotly as plotting backend (dropped matplotlib) | ||
|
|
||
| 1.2.1 (2016-07-26) | ||
| ~~~~~~~~~~~~~~~~~~ | ||
|
|
||
| - Updated changelog, fix version number in documentation | ||
|
|
||
| 1.2.4 (2016-08-04) | ||
| ~~~~~~~~~~~~~~~~~~ | ||
|
|
||
| - Fixed bug that made it impossible to run GO-PCA from the command line | ||
| (`go-pca.py`) | ||
|
|
||
| 1.2.5 (2016-08-05) | ||
| ~~~~~~~~~~~~~~~~~~ | ||
|
|
||
| - Fixed a bug that prevented the Gene Ontology file from being loaded when | ||
| running GO-PCA from the command line (`go-pca.py`) | ||
|
|
||
| Version 1.1.3 (2016-02-23) | ||
| -------------------------- | ||
|
|
||
| - Added a lot more documentation (see http://gopca.readthedocs.org). | ||
| - Added ``gopca_plot_all_signatures.py`` command. | ||
|
|
||
| Version 1.1.2 (2016-02-04) | ||
| -------------------------- | ||
|
|
||
| - Fixed a bug in the local filter that resulted in incorrect filtering | ||
|
|
||
| Version 1.1.0 (2016-02-02) | ||
| -------------------------- | ||
| - Restructured the documentation (work still ongoing). | ||
| - The "GO annotation file" is now more accurately being referred to as | ||
| "gene set file" | ||
| - Modified file format for supplying gene sets (added a "description" column) | ||
| - GO-PCA is intended to work with arbitrary gene sets, and the code now | ||
| reflects this as well (parameter names, variable names, etc.) | ||
| - Added support for INI-style GO-PCA configuration file ("go-pca.py -c ...") | ||
| - Improved documentation of command-line pamaraters ("go-pca.py --help") | ||
| - Improved support for config and result MD5 hash values | ||
| (they are now shown by "gopca_print_info.py") | ||
|
|
||
| Version 1.1rc12 | ||
| --------------- | ||
| - Reorganized internal class structure (see `GOPCARun` in ``run.py``) | ||
| - Added Unicode support | ||
| - Added ``gopca_print_info.py`` script to quickly inspect GO-PCA output data | ||
|
|
||
| Version 1.1rc10 | ||
| --------------- | ||
|
|
||
| - Fixed a bug that occurred when no ontology file is given. | ||
|
|
||
| Version 1.1rc9 | ||
| -------------- | ||
|
|
||
| "Visible" changes: | ||
|
|
||
| - Changed the names of some command line arguments. | ||
| - Added/improved documentation of command line parameters for all scripts. | ||
| - Changed the sphinx html documentation theme to bootstrap | ||
| ("sphinx-bootstrap-theme"). | ||
|
|
||
| Internal changes: | ||
|
|
||
| - Improved code documentation. | ||
| - The GO-PCA parameters `disable_local_filter` and `disable_global_filter` are | ||
| now called `no_nocal_filter` and `no_global_filter`, respectively. | ||
| - The expression matrix is now represented using the `ExpMatrix` class from the | ||
| `genometools` package. | ||
| - Shared parameter for plotting scripts are now obtained using functions from | ||
| the `plotting.params` module (this greatly reduced code redundancy). | ||
| - Loggers are no longer class members, and are instead defined as global | ||
| variables within each module. This is consistent with the recommended naming | ||
| scheme that uses `logging.getLogger(__name__)`, thus naming a logger after | ||
| the module. This helped to simplify the class structures. | ||
| - Made the following command-line scripts work again (and added tests): | ||
|
|
||
| - gopca_print_info.py | ||
| - gopca_extract_signatures.py | ||
| - gopca_extract_signatures_excel.py | ||
| - gopca_extract_signature_matrix.py | ||
| - gopca_plot_signature_matrix.py | ||
|
|
||
| - Updated section on the command-line interace in the documentation, and added | ||
| it to the table of contents. | ||
|
|
||
| - Internals: | ||
|
|
||
| - Changed naming scheme of some source files (main.py => cli/go_pca.py, | ||
| go_pca.py => gopca.py) |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,167 @@ | ||
| .. | ||
| Copyright (c) 2015, 2016 Florian Wagner | ||
| This file is part of GO-PCA. | ||
| GO-PCA is free software: you can redistribute it and/or modify | ||
| it under the terms of the GNU Affero General Public License, Version 3, | ||
| as published by the Free Software Foundation. | ||
| This program is distributed in the hope that it will be useful, | ||
| but WITHOUT ANY WARRANTY; without even the implied warranty of | ||
| MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the | ||
| GNU Affero General Public License for more details. | ||
| You should have received a copy of the GNU Affero General Public License | ||
| along with this program. If not, see <http://www.gnu.org/licenses/>. | ||
|
|
||
| Changelog | ||
| ========= | ||
|
|
||
| Version 2.1.0 (2016-08-28) | ||
| -------------------------- | ||
|
|
||
| - Improved algorithm for generating signatures based on significantly enriched | ||
| gene sets, and introduced a new parameter, ``sig_min_genes`` to specify the | ||
| minimum number of genes in each signature. Effectively, this makes gene set | ||
| enrichment analysis and signature generation more independent of each other, | ||
| and results in more coherent signatures (i.e., genes in a signature should | ||
| have more similar expression patterns with the new algorithm). | ||
|
|
||
| - Improved the "Installing GO-PCA" section of the documentation. The section | ||
| now includes accurate instructions for Windows and Mac OS X. | ||
|
|
||
| - Reduced the verbosity of GO-PCA output. The old verbosity can be restored | ||
| by passing ``verbose=True`` to GO-PCA, or by running the ``go-pca.py`` script | ||
| with the ``-v`` option. | ||
|
|
||
| - Changed data structure used for representing signature matrices | ||
| (`GOPCASignatureMatrix` now inherits from `genometools.expression.ExpMatrix`). | ||
|
|
||
| - Added simplified functions for plotting heatmaps of signature matrices | ||
| and signature genes to the Python API: `GOPCASignatureMatrix.get_figure()` | ||
| and `GOPCASignature.get_figure()`. | ||
|
|
||
| 2.1.1 (2016-09-04) | ||
| ~~~~~~~~~~~~~~~~~~ | ||
|
|
||
| - Travis deploy step now generates and uploads wheels. | ||
| - Fixed bug in `GOPCASignatureMatrix.filter_collection_signatures()`. | ||
|
|
||
| 2.1.2 (2016-09-04) | ||
| ~~~~~~~~~~~~~~~~~~ | ||
|
|
||
| - Changed genometools dependency to version 2.0.2. | ||
|
|
||
| 2.1.3 (2016-09-04) | ||
| ~~~~~~~~~~~~~~~~~~ | ||
|
|
||
| - Renamed `GOPCA.simple_init()` to `simple_setup()`. | ||
|
|
||
| 2.1.4 (2016-10-06) | ||
| ------------------ | ||
|
|
||
| - Modified `GOPCASignature.get_figure()` call signature. | ||
|
|
||
| Version 2.0.0 (2016-08-01) | ||
| -------------------------- | ||
|
|
||
| - Generalized the API to support multiple "configurations" as input. Each | ||
| configuration (`GOPCAConfig`) consists of a set of GO-PCA parameters | ||
| (`GOPCAParams`), a list of gene sets | ||
| (`genometools.basic.GeneSetCollection`), and, optionally, a gene ontology | ||
| (`genometools.ontology.GeneOntology`). GO-PCA is performed independently | ||
| for each configuration, and the signatures generated are merged into a | ||
| single signature matrix. The old way of configuring GO-PCA is available as | ||
| `GOPCA.simple_setup()`. | ||
|
|
||
| Version 2.0.1 (2016-08-16) | ||
| ~~~~~~~~~~~~~~~~~~~~~~~~~~ | ||
| - Some bugfixes | ||
|
|
||
| Version 1.2.0 (2016-07-26) | ||
| -------------------------- | ||
|
|
||
| - Full Python 3.5 support (on top of Python 2.7) | ||
| - New Python API for running GO-PCA, accessing results and generating figures | ||
| - Integrated code with genometools 2.0 | ||
| - Cleaned up code | ||
| - Added tests (using py.test) | ||
| - Switched to plotly as plotting backend (dropped matplotlib) | ||
|
|
||
| 1.2.1 (2016-07-26) | ||
| ~~~~~~~~~~~~~~~~~~ | ||
|
|
||
| - Updated changelog, fix version number in documentation | ||
|
|
||
| 1.2.4 (2016-08-04) | ||
| ~~~~~~~~~~~~~~~~~~ | ||
|
|
||
| - Fixed bug that made it impossible to run GO-PCA from the command line | ||
| (`go-pca.py`) | ||
|
|
||
| 1.2.5 (2016-08-05) | ||
| ~~~~~~~~~~~~~~~~~~ | ||
|
|
||
| - Fixed a bug that prevented the Gene Ontology file from being loaded when | ||
| running GO-PCA from the command line (`go-pca.py`) | ||
|
|
||
| Version 1.1.3 (2016-02-23) | ||
| -------------------------- | ||
|
|
||
| - Added a lot more documentation (see http://gopca.readthedocs.org). | ||
| - Added ``gopca_plot_all_signatures.py`` command. | ||
|
|
||
| Version 1.1.2 (2016-02-04) | ||
| -------------------------- | ||
|
|
||
| - Fixed a bug in the local filter that resulted in incorrect filtering | ||
|
|
||
| Version 1.1.0 (2016-02-02) | ||
| -------------------------- | ||
| - Restructured the documentation (work still ongoing). | ||
| - The "GO annotation file" is now more accurately being referred to as | ||
| "gene set file" | ||
| - Modified file format for supplying gene sets (added a "description" column) | ||
| - GO-PCA is intended to work with arbitrary gene sets, and the code now | ||
| reflects this as well (parameter names, variable names, etc.) | ||
| - Added support for INI-style GO-PCA configuration file ("go-pca.py -c ...") | ||
| - Improved documentation of command-line pamaraters ("go-pca.py --help") | ||
| - Improved support for config and result MD5 hash values | ||
| (they are now shown by "gopca_print_info.py") | ||
|
|
||
| Version 1.1rc12 | ||
| --------------- | ||
| - Reorganized internal class structure (see `GOPCARun` in ``run.py``) | ||
| - Added Unicode support | ||
| - Added ``gopca_print_info.py`` script to quickly inspect GO-PCA output data | ||
|
|
||
| Version 1.1rc10 | ||
| --------------- | ||
|
|
||
| - Fixed a bug that occurred when no ontology file is given. | ||
|
|
||
| Version 1.1rc9 | ||
| -------------- | ||
|
|
||
| "Visible" changes: | ||
|
|
||
| - Changed the names of some command line arguments. | ||
| - Added/improved documentation of command line parameters for all scripts. | ||
| - Changed the sphinx html documentation theme to bootstrap | ||
| ("sphinx-bootstrap-theme"). | ||
|
|
||
| Internal changes: | ||
|
|
||
| - Improved code documentation. | ||
| - The GO-PCA parameters `disable_local_filter` and `disable_global_filter` are | ||
| now called `no_nocal_filter` and `no_global_filter`, respectively. | ||
| - The expression matrix is now represented using the `ExpMatrix` class from the | ||
| `genometools` package. | ||
| - Shared parameter for plotting scripts are now obtained using functions from | ||
| the `plotting.params` module (this greatly reduced code redundancy). | ||
| - Loggers are no longer class members, and are instead defined as global | ||
| variables within each module. This is consistent with the recommended naming | ||
| scheme that uses `logging.getLogger(__name__)`, thus naming a logger after | ||
| the module. This helped to simplify the class structures. |
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