From 62ec322abda3869bb10e81635a077390ecf0820f Mon Sep 17 00:00:00 2001
From: Aurelie Mercadie <aurelie.mercadie@inrae.fr>
Date: Thu, 22 Aug 2024 13:31:58 +0200
Subject: [PATCH 1/5] initialized CHANGELOG.md
---
CHANGELOG.md | 10 ++++++++++
1 file changed, 10 insertions(+)
create mode 100644 CHANGELOG.md
diff --git a/CHANGELOG.md b/CHANGELOG.md
new file mode 100644
index 0000000..43c2ddc
--- /dev/null
+++ b/CHANGELOG.md
@@ -0,0 +1,10 @@
+# Changelog
+All notable changes to this project will be documented in this file.
+
+The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
+and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+
+## [Unreleased]
+
+## [0.2.0] - 2024-08-22
+- issue during module import
\ No newline at end of file
--
GitLab
From b4d84886022edde62797f645813bdbbcb1911b46 Mon Sep 17 00:00:00 2001
From: Aurelie Mercadie <aurelie.mercadie@inrae.fr>
Date: Thu, 22 Aug 2024 13:40:40 +0200
Subject: [PATCH 2/5] added links for PyPI
---
pyproject.toml | 2 ++
1 file changed, 2 insertions(+)
diff --git a/pyproject.toml b/pyproject.toml
index 1d716e0..09914f1 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -65,6 +65,8 @@ dev = ["black", "bump2version", "isort", "pip-tools", "pytest"]
[project.urls]
Homepage = "https://forgemia.inra.fr/omics-integration/nmfprofiler"
+Documentation = "https://omics-integration.pages.mia.inra.fr/nmfprofiler"
+Changelog = "https://forgemia.inra.fr/omics-integration/nmfprofiler/-/blob/dev/CHANGELOG.md"
[project.scripts]
NMFProfilerpython = "NMFProfiler.__main__:main" # command-line script that calls the main function
--
GitLab
From a9ea1c2d1844633bb4f3d619608e2f35e001128b Mon Sep 17 00:00:00 2001
From: Aurelie Mercadie <aurelie.mercadie@inrae.fr>
Date: Thu, 22 Aug 2024 14:31:45 +0200
Subject: [PATCH 3/5] fixed module inclusion + minor changes
---
pyproject.toml | 6 ++----
1 file changed, 2 insertions(+), 4 deletions(-)
diff --git a/pyproject.toml b/pyproject.toml
index 09914f1..9b1d731 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -38,8 +38,6 @@ maintainers = [
]
license = { file = "LICENSE" }
classifiers = [
- "Development Status :: 3 - Alpha",
- "Framework :: Jupyter",
"Intended Audience :: Science/Research",
"License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)",
"Operating System :: Microsoft :: Windows", # precise which version exactly used at PF
@@ -66,10 +64,10 @@ dev = ["black", "bump2version", "isort", "pip-tools", "pytest"]
[project.urls]
Homepage = "https://forgemia.inra.fr/omics-integration/nmfprofiler"
Documentation = "https://omics-integration.pages.mia.inra.fr/nmfprofiler"
-Changelog = "https://forgemia.inra.fr/omics-integration/nmfprofiler/-/blob/dev/CHANGELOG.md"
+Changelog = "https://forgemia.inra.fr/omics-integration/nmfprofiler/-/blob/main/CHANGELOG.md"
[project.scripts]
NMFProfilerpython = "NMFProfiler.__main__:main" # command-line script that calls the main function
[tool.setuptools.packages.find]
-include = ["nmfprofiler"] # package names should match these glob patterns (["*"] by default)
+include = ["nmfprofiler","nmfprofiler.utils"] # package names should match these glob patterns (["*"] by default)
--
GitLab
From 2dc1e9f06b74d16092d318a51a139c1f6aa3b183 Mon Sep 17 00:00:00 2001
From: Nathalie Vialaneix <nathalie.vialaneix@inrae.fr>
Date: Fri, 23 Aug 2024 09:31:30 +0200
Subject: [PATCH 4/5] slightly improved changelog and added a link in README
---
CHANGELOG.md | 19 ++++++++++++++++---
README.md | 2 ++
2 files changed, 18 insertions(+), 3 deletions(-)
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 43c2ddc..158dc8a 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -4,7 +4,20 @@ All notable changes to this project will be documented in this file.
The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
-## [Unreleased]
+## [0.1.0] - 2024-07-24 (unpublished)
+- initial release
+
+## [0.2.0] - 2024-08-22 (first published release)
+- improved documentation
+- added vignette
+- added data loader
+- turned heatmap as a method
+- fixed some options
+- added input checks
+- **Do not use this release!** It is missing a module.
+
+## [0.2.1] - 2024-08-23
+- bug fixes: added missing module
+- added Changelog (this file)
+- slightly improved documentation
-## [0.2.0] - 2024-08-22
-- issue during module import
\ No newline at end of file
diff --git a/README.md b/README.md
index 0da5ced..644ae73 100644
--- a/README.md
+++ b/README.md
@@ -85,3 +85,5 @@ GPL-3
## Project status
Active
+
+See [Changelog](https://forgemia.inra.fr/omics-integration/nmfprofiler/-/blob/main/CHANGELOG.md)
--
GitLab
From 18ebb53b45c39dc2e11c7411ebf327e02b3a9f2a Mon Sep 17 00:00:00 2001
From: Nathalie Vialaneix <nathalie.vialaneix@inrae.fr>
Date: Fri, 23 Aug 2024 09:31:47 +0200
Subject: [PATCH 5/5] bumped version number and dates
---
codemeta.json | 6 +++---
docs/source/conf.py | 2 +-
pyproject.toml | 2 +-
3 files changed, 5 insertions(+), 5 deletions(-)
diff --git a/codemeta.json b/codemeta.json
index 5e873c7..030de6a 100644
--- a/codemeta.json
+++ b/codemeta.json
@@ -4,10 +4,10 @@
"license": "https://spdx.org/licenses/GPL-3.0",
"codeRepository": "https://forgemia.inra.fr/omics-integration/nmfprofiler",
"dateCreated": "2024-06-24",
- "datePublished": "2024-06-24",
- "dateModified": "2024-08-22",
+ "datePublished": "2024-08-22",
+ "dateModified": "2024-08-23",
"name": "NMFProfiler",
- "version": "0.2",
+ "version": "0.2.1",
"description": "NMFProfiler: an integrative supervised Non-Negative Matrix Factorization to extract typical profiles of groups of interest combining two different datasets.",
"applicationCategory": "Biostatistics",
"funding": "2022/0051",
diff --git a/docs/source/conf.py b/docs/source/conf.py
index 3177138..cead502 100644
--- a/docs/source/conf.py
+++ b/docs/source/conf.py
@@ -21,7 +21,7 @@ sys.path.insert(0, os.path.abspath("../.."))
project = "NMFProfiler"
copyright = "2024, Aurélie Mercadié"
author = "Aurélie Mercadié"
-release = "0.2"
+release = "0.2.1"
# -- General configuration ---------------------------------------------------
# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
diff --git a/pyproject.toml b/pyproject.toml
index 9b1d731..13746f6 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -22,7 +22,7 @@ build-backend = "setuptools.build_meta"
[project]
name = "NMFProfiler"
-version = "0.2"
+version = "0.2.1"
description = "NMFProfiler: an integrative supervised Non-Negative Matrix Factorization to extract typical profiles of groupes of interest combining two different datasets."
readme = "README.md"
authors = [
--
GitLab