From 929ecdc59c39c8ad5b5b1c343c31167c9d62078b Mon Sep 17 00:00:00 2001
From: Lukas Pielsticker <50139597+lukaspie@users.noreply.github.com>
Date: Mon, 6 May 2024 15:10:43 +0200
Subject: [PATCH 1/3] add plugin and links to individual docs to the main docs
---
README.md | 24 ------------------------
docs/index.md | 4 +++-
docs/reference/plugins.md | 25 +++++++++++++++++++++++++
pynxtools/definitions | 2 +-
4 files changed, 29 insertions(+), 26 deletions(-)
create mode 100644 docs/reference/plugins.md
diff --git a/README.md b/README.md
index be0680360..da079e7af 100644
--- a/README.md
+++ b/README.md
@@ -52,30 +52,6 @@ data into the NeXus standard and visualising the files content.
# Documentation
Documentation for the different tools can be found [here](https://fairmat-nfdi.github.io/pynxtools/).
-# Plugins
-There are a number of plugins available for pynxtools. These are extensions of pynxtools used for reading data of specific experimental techniques.
-- [**pynxtools-mpes**](https://github.com/FAIRmat-NFDI/pynxtools-mpes): A reader for multi-dimensional photoelectron spectroscopy data.
-- [**pynxtools-stm**](https://github.com/FAIRmat-NFDI/pynxtools-stm): A reader for scanning tunneling microscopy (SPM) and spectroscopy (STS) data.
-- [**pynxtools-xps**](https://github.com/FAIRmat-NFDI/pynxtools-xps): A reader for X-ray photoelectron spectroscopy (XPS) data.
-- [**pynxtools-apm**](https://github.com/FAIRmat-NFDI/pynxtools-apm): A reader for atom probe as well as related field ion microscopy data.
-- [**pynxtools-em**](https://github.com/FAIRmat-NFDI/pynxtools-em): A reader for electron microscopy data.
-- [**pynxtools-ellips**](https://github.com/FAIRmat-NFDI/pynxtools-ellips): A reader for ellipsometry data.
-
-Note that pynxtools-apm and pynxtools-em are currently refactored into pynxtools plugins.
-Until this refactoring will have become completed, users are advised to use the apm and em readers via pynxtools<=0.1.1.
-
-
-You can install each of the plugins together with `pynxtools` by passing the name of the plugin as an extra to the pip install call. For example, for the `pynxtools-mpes` plugin:
-```shell
-pip install pynxtools[mpes]
-```
-
-In addition, you can also install all of the `pynxtools` reader plugins which are maintained by FAIRmat by passing the `[convert]` extra to the pip install call:
-```shell
-pip install pynxtools[convert]
-```
-There is also a [cookiecutter template](https://github.com/FAIRmat-NFDI/pynxtools-plugin-template) available for creating your own pynxtools plugin.
-
# Contributing
## Development install
diff --git a/docs/index.md b/docs/index.md
index 7b9e44a08..3dd79f389 100644
--- a/docs/index.md
+++ b/docs/index.md
@@ -51,6 +51,8 @@ An introduction to NeXus and its design principles.
### Reference
+Within FAIRmat, we maintain a number of reader plugins for different experimental techniques. You can find more information [here](reference/plugins.md).
+
[Here](reference/definitions.md), you find the detailed list of application definitions and base classes and their respective fields.
Or go directly to the [official NIAC](https://manual.nexusformat.org/classes/index.html)
@@ -59,4 +61,4 @@ Or go directly to the [official NIAC](https://manual.nexusformat.org/classes/ind
-Project and community
+Project and community
\ No newline at end of file
diff --git a/docs/reference/plugins.md b/docs/reference/plugins.md
new file mode 100644
index 000000000..07178ba23
--- /dev/null
+++ b/docs/reference/plugins.md
@@ -0,0 +1,25 @@
+# Plugins
+There are a number of plugins available for pynxtools that are maintained within FAIRmat. These are extensions of pynxtools used for reading data of specific experimental techniques.
+
+- [**pynxtools-mpes**](https://github.com/FAIRmat-NFDI/pynxtools-mpes): A reader for multi-dimensional photoelectron spectroscopy data.
+- [**pynxtools-stm**](https://github.com/FAIRmat-NFDI/pynxtools-stm): A reader for scanning tunneling microscopy (SPM) and spectroscopy (STS) data.
+- [**pynxtools-xps**](https://github.com/FAIRmat-NFDI/pynxtools-xps): A reader for X-ray photoelectron spectroscopy (XPS) data. Documentation can be found [here](https://fairmat-nfdi.github.io/pynxtools-xps/).
+- [**pynxtools-apm**](https://github.com/FAIRmat-NFDI/pynxtools-apm): A reader for atom probe as well as related field ion microscopy data. Documentation can be found [here](https://fairmat-nfdi.github.io/pynxtools-apm/).
+- [**pynxtools-em**](https://github.com/FAIRmat-NFDI/pynxtools-em): A reader for electron microscopy data. Documentation can be found [here](https://fairmat-nfdi.github.io/pynxtools-em/).
+- [**pynxtools-ellips**](https://github.com/FAIRmat-NFDI/pynxtools-ellips): A reader for ellipsometry data. Documentation can be found [here](https://fairmat-nfdi.github.io/pynxtools-ellips/).
+
+## Installation
+
+You can install each of the plugins together with pynxtools by passing the name of the plugin as an extra to the pip install call. For example, for the pynxtools-mpes plugin:
+
+```
+pip install pynxtools[mpes]
+```
+
+In addition, you can also install all of the pynxtools reader plugins which are maintained by FAIRmat by passing the [convert] extra to the pip install call:
+
+```
+pip install pynxtools[convert]
+```
+
+There is also a [cookiecutter template](https://github.com/FAIRmat-NFDI/pynxtools-plugin-template) available for creating your own pynxtools plugin.
diff --git a/pynxtools/definitions b/pynxtools/definitions
index 229774c56..65ab98b9c 160000
--- a/pynxtools/definitions
+++ b/pynxtools/definitions
@@ -1 +1 @@
-Subproject commit 229774c56fb710bb1d9008afb49e00be402c7578
+Subproject commit 65ab98b9c7f63e42c8013bdba1141f687ae67594
From 836635ffa9f7177a7163954eb4cbcb42d6f70073 Mon Sep 17 00:00:00 2001
From: Lukas Pielsticker <50139597+lukaspie@users.noreply.github.com>
Date: Mon, 6 May 2024 15:12:55 +0200
Subject: [PATCH 2/3] correct reference in mkdocs.yaml
---
mkdocs.yaml | 1 +
1 file changed, 1 insertion(+)
diff --git a/mkdocs.yaml b/mkdocs.yaml
index f02641f6a..35a254020 100644
--- a/mkdocs.yaml
+++ b/mkdocs.yaml
@@ -14,6 +14,7 @@ nav:
- learn/nexus-primer.md
- learn/multiple-appdefs.md
- Reference:
+ - reference/plugins.md
- reference/definitions.md
theme:
name: material
From bd77a36e42f11ae209ed46fce81f06e69219e849 Mon Sep 17 00:00:00 2001
From: Lukas Pielsticker <50139597+lukaspie@users.noreply.github.com>
Date: Mon, 6 May 2024 16:30:22 +0200
Subject: [PATCH 3/3] update definitions to fit with master branch
---
pynxtools/definitions | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/pynxtools/definitions b/pynxtools/definitions
index 65ab98b9c..229774c56 160000
--- a/pynxtools/definitions
+++ b/pynxtools/definitions
@@ -1 +1 @@
-Subproject commit 65ab98b9c7f63e42c8013bdba1141f687ae67594
+Subproject commit 229774c56fb710bb1d9008afb49e00be402c7578