get-rid-of-github-path-in-dependencies

README.md

@@ -35,15 +35,61 @@ nomad-ikz-plugin/
 
 ## Installation
 
-To use the plugin, you need to clone this repo in your local machine and install the package with pip:
-
-```bash
-git clone https://github.com/IKZ-Berlin/nomad-ikz-plugin
-cd nomad-ikz-plugin
-pip install -e .[dev]
-```
-
-For more details on what happens under the hood, check the `.toml` file in the `nomad-ikz-plugin` folder:
+To use this plugin you need to install several dependent packages.
+
+There are at least two ways of installing them, depending on your aim:
+
+- Deploy a custom NOMAD Oasis image.
+  Refer to the [IKZ NOMAD Oasis custom image](https://github.com/IKZ-Berlin/nomad-oasis-ikz/tree/main) to discover how the `pyproject.toml` is composed.
+  You will need the following lines to fulfill the dependencies of this plugin:
+
+  ```
+  [project.optional-dependencies]
+  plugins = [
+    "nomad-material-processing @ git+https://github.com/FAIRmat-NFDI/nomad-material-processing.git@8545ef374ac53169fe1e40be927a212a364ebda1",
+    "nomad-measurements @ git+https://github.com/FAIRmat-NFDI/nomad-measurements.git@237dd2b6fc6152dbb8370a24dce26e483fb8ba78",
+    "nomad-analysis @ git+https://github.com/FAIRmat-NFDI/nomad-analysis.git@7f2fe10084953e2827389e2bcb42df6b106ab484",
+    "nomad-ikz-plugin",
+    "uv_vis_nir_transmission @ git+https://github.com/FAIRmat-NFDI/AreaA-data_modeling_and_schemas.git@245a82ddc24da5f8aaa79164e6669c18c2bc1572#subdirectory=transmission/transmission_plugin/uv_vis_nir_transmission_plugin",
+    "lakeshore-nomad-plugin @ git+https://github.com/IKZ-Berlin/lakeshore-nomad-plugin.git@69a6deb3f0e99d7b0dc66714105dd62a56f157e9",
+    "laytec_epitt_plugin @ git+https://github.com/IKZ-Berlin/laytec_epitt_nomad_plugin.git@f4953ac4ecb55b7003dee323d7d7f473e49ab4e3",
+    "statsmodels" 
+    ]
+    [tool.uv.sources]
+    nomad-ikz-plugin = { git = "https://github.com/IKZ-Berlin/nomad-ikz-plugin.git", rev = "v0.1.2" }
+  ```
+
+> [!NOTE]
+> the toml above shows that the `nomad-ikz-plugin` is not bound to a commit, rather to a release
+
+- Develop the plugin in your development environment.
+  Refer to the [nomad-distro-dev repository](https://github.com/FAIRmat-NFDI/nomad-distro-dev) to setup your environment.
+  You will then need to add all the dependencies as submodules and also to use the uv command `add` to have them in your python env.
+
+  ```
+  git submodule add https://github.com/FAIRmat-NFDI/nomad-measurements packages/nomad-measurements
+  git submodule add https://github.com/FAIRmat-NFDI/nomad-material-processing packages/nomad-material-processing
+  git submodule add https://github.com/IKZ-Berlin/nomad-ikz-plugin packages/nomad-ikz-plugin
+  git submodule add https://github.com/IKZ-Berlin/laytec_epitt_nomad_plugin packages/laytec_epitt_nomad_plugin
+  git submodule add https://github.com/IKZ-Berlin/lakeshore-nomad-plugin packages/lakeshore-nomad-plugin
+  git submodule update --init --recursive
+  uv add packages/nomad-ikz-plugin
+  uv add packages/lakeshore-nomad-plugin
+  uv add packages/laytec_epitt_nomad_plugin
+  uv add packages/nomad-measurements
+  uv add packages/nomad-material-processing 
+  ```
+
+- Pip install everything manually (also nomad-lab)
+    You need to clone this repo in your local machine and install the package with pip:
+
+    ```bash
+    git clone https://github.com/IKZ-Berlin/nomad-ikz-plugin
+    cd nomad-ikz-plugin
+    pip install -e .[dev]
+    ```
+
+For more details on what happens in this plugin under the hood, check the `.toml` file in the `nomad-ikz-plugin` folder:
 
 - all the installed subpackages are listed under the section `[project.entry-points.'nomad.plugin']`.
 - `dependencies` and `[project.optional-dependencies]` contain all the other packages installed along to this one.

pyproject.toml

@@ -33,10 +33,10 @@ dependencies = [
     'nomad-material-processing',
     'nomad-measurements',
     'nomad-analysis', # develop branch
-    'lakeshore-nomad-plugin @ git+https://github.com/IKZ-Berlin/lakeshore-nomad-plugin.git@69a6deb3f0e99d7b0dc66714105dd62a56f157e9',
-    'laytec_epitt_plugin @ git+https://github.com/IKZ-Berlin/laytec_epitt_nomad_plugin.git@f4953ac4ecb55b7003dee323d7d7f473e49ab4e3',
-    'transmission @ git+https://github.com/FAIRmat-NFDI/AreaA-data_modeling_and_schemas.git@2b2c38809e63e3578ef63d8c1d1fe9e27aa7a321#subdirectory=transmission/transmission_plugin/uv_vis_nir_transmission_plugin',
-]
+    'lakeshore-nomad-plugin', 
+    'laytec_epitt_plugin',
+    'transmission @ git+https://github.com/FAIRmat-NFDI/AreaA-data_modeling_and_schemas.git@main#subdirectory=transmission/transmission_plugin/uv_vis_nir_transmission_plugin',
+    ]
 
 [project.optional-dependencies]
 dev = [