From 63ac845b2e1afdf6fc79466c1feafdd34538bb10 Mon Sep 17 00:00:00 2001
From: Steph Prince <40640337+stephprince@users.noreply.github.com>
Date: Wed, 31 Jul 2024 00:46:10 -0700
Subject: [PATCH 1/4] fix versioning guidelines link (#586)

---
 docs/format/source/software_process.rst | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/format/source/software_process.rst b/docs/format/source/software_process.rst
index 49996cd5..3640be28 100644
--- a/docs/format/source/software_process.rst
+++ b/docs/format/source/software_process.rst
@@ -130,5 +130,5 @@ released version of nwb-schema. Starting with nwb-schema version 2.2.0, the dev
 and MatNWB include only publicly released versions of nwb-schema. For more details, see the
 [PyNWB software process documentation](https://pynwb.readthedocs.io/en/stable/software_process.html).
 
-The [NWB Extensions Versioning Guidelines](https://nwb-extensions.github.io/versioning_guidelines) are used to guide
+The [NWB Extensions Versioning Guidelines](https://www.nwb.org/versioning-guidelines) are used to guide
 versioning of the NWB core schema, as well as extensions to NWB.

From 67bcded95a685173235c70b7ee7c3d80734c01b7 Mon Sep 17 00:00:00 2001
From: Steph Prince <40640337+stephprince@users.noreply.github.com>
Date: Thu, 19 Sep 2024 14:45:02 -0700
Subject: [PATCH 2/4] Add dataset to store list of software that produced a
 file (#578)

* add nwbfile dataset for provenance information

* update software version dataset name and doc

* update release notes
---
 core/nwb.file.yaml                          | 12 ++++++++++++
 docs/format/source/format_release_notes.rst |  2 +-
 2 files changed, 13 insertions(+), 1 deletion(-)

diff --git a/core/nwb.file.yaml b/core/nwb.file.yaml
index 3997cc23..f3232ed0 100644
--- a/core/nwb.file.yaml
+++ b/core/nwb.file.yaml
@@ -241,6 +241,18 @@ groups:
       - name: file_name
         dtype: text
         doc: Name of script file.
+    - name: was_generated_by
+      dtype: text
+      doc: Name and version of software package(s) used to generate data contained in
+       this NWB File. For each software package or library, include the name of the
+       software as the first value and the version as the second value.
+      dims:
+      - num_sources
+      - name, version
+      shape:
+      - null
+      - 2
+      quantity: '?'
     - name: stimulus
       dtype: text
       doc: Notes about stimuli, such as how and where they were presented.
diff --git a/docs/format/source/format_release_notes.rst b/docs/format/source/format_release_notes.rst
index b5b837e0..74225e4e 100644
--- a/docs/format/source/format_release_notes.rst
+++ b/docs/format/source/format_release_notes.rst
@@ -12,7 +12,7 @@ Minor changes
   ``waveform_sd`` columns ragged. This allows for a different number of waveform means/SDs per unit which is useful
   when each unit is associated with a different number of electrodes and there is a waveform mean/SD for each
   electrode and unit. (#576)
-
+- Added optional ``was_generated_by`` attribute to ``NWBFile`` to store provenance information (#578)
 
 2.7.0 (February 7, 2024)
 ------------------------

From 1c64325bb97f5a1fedb09433b5cfdc6d044ee01a Mon Sep 17 00:00:00 2001
From: Steph Prince <40640337+stephprince@users.noreply.github.com>
Date: Thu, 19 Sep 2024 17:08:22 -0700
Subject: [PATCH 3/4] Create .readthedocs.yaml (#590)

---
 docs/storage/.readthedocs.yaml | 27 +++++++++++++++++++++++++++
 1 file changed, 27 insertions(+)
 create mode 100644 docs/storage/.readthedocs.yaml

diff --git a/docs/storage/.readthedocs.yaml b/docs/storage/.readthedocs.yaml
new file mode 100644
index 00000000..78614ac1
--- /dev/null
+++ b/docs/storage/.readthedocs.yaml
@@ -0,0 +1,27 @@
+# Read the Docs configuration file for https://nwb-storage.readthedocs.io/en/latest/
+ # See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+ # Required
+ version: 2
+
+ build:
+   os: ubuntu-22.04
+   tools:
+     python: "3.12"
+
+ # Build documentation in the docs/ directory with Sphinx
+ sphinx:
+   configuration: docs/storage/source/conf.py
+
+ # Optionally build your docs in additional formats such as PDF and ePub
+ formats: all
+
+ # Optionally set the version of Python and requirements required to build your docs
+ python:
+   install:
+     - requirements: requirements-doc.txt
+
+ # Optionally include all submodules
+ submodules:
+   include: all
+   recursive: true

From f11b765313eb2594862f835d66d515f3345e381d Mon Sep 17 00:00:00 2001
From: Ryan Ly <rly@lbl.gov>
Date: Thu, 19 Sep 2024 17:16:27 -0700
Subject: [PATCH 4/4] Fix storage RTD for newer sphinx (#591)

---
 docs/storage/source/conf.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/storage/source/conf.py b/docs/storage/source/conf.py
index 2f4a3219..409d167b 100644
--- a/docs/storage/source/conf.py
+++ b/docs/storage/source/conf.py
@@ -105,7 +105,7 @@
 html_theme_path = [sphinx_rtd_theme.get_html_theme_path()]
 
 def setup(app):
-   app.add_stylesheet("theme_overrides.css")  # overrides for wide tables in RTD theme
+   app.add_css_file("theme_overrides.css")  # overrides for wide tables in RTD theme
 
 # Theme options are theme-specific and customize the look and feel of a theme
 # further.  For a list of options available for each theme, see the