From b478a4b98985aaab95de7dbf729d31f31eb8eccd Mon Sep 17 00:00:00 2001
From: Oliver Bertuch <o.bertuch@fz-juelich.de>
Date: Thu, 12 Jan 2023 17:13:51 +0100
Subject: [PATCH 01/21] docs: initial draft of first user tutorial

---
 docs/source/index.md                          |   8 +
 .../tutorials/001-prepare-your-project.md     | 149 ++++++++++++++++++
 2 files changed, 157 insertions(+)
 create mode 100644 docs/source/tutorials/001-prepare-your-project.md

diff --git a/docs/source/index.md b/docs/source/index.md
index 5509e203..53e8261a 100644
--- a/docs/source/index.md
+++ b/docs/source/index.md
@@ -15,6 +15,14 @@ This is a work in progress. Expect disruptive changes.
 ```{include} ../../README.md
 ```
 
+## Tutorials
+ 
+```{toctree}
+:glob:
+:maxdepth: 1
+tutorials/*
+```
+
 ## Developer Documentation
 
 ```{toctree}
diff --git a/docs/source/tutorials/001-prepare-your-project.md b/docs/source/tutorials/001-prepare-your-project.md
new file mode 100644
index 00000000..4c1b2732
--- /dev/null
+++ b/docs/source/tutorials/001-prepare-your-project.md
@@ -0,0 +1,149 @@
+<!--
+SPDX-FileCopyrightText: 2022 German Aerospace Center (DLR)
+
+SPDX-License-Identifier: CC-BY-SA-4.0
+-->
+
+<!-- 
+SPDX-FileContributor: Michael Meinel
+-->
+
+# Tutorial 1: Make your project compatible with Hermes
+ 
+In this tutorial we will guide you through the process of preparing your project for metadata publication.
+We assume that you have a project that is stored in a Git repository.
+There is no obvious additional metadata available.
+ 
+We use https://github.com/hermes-hmc/base-example throughout this tutorial.
+It should be easily adoptable to other repositories.
+ 
+## Clone the repository
+ 
+This step is optional if you use a checked-out version of your own repository.
+ 
+```
+git clone https://github.com/hermes-hmc/base-example.git
+cd base-example
+```
+ 
+Your directory should look like the following:
+ 
+...
+ 
+## Test-drive hermes
+ 
+Even though there is no metadata stored yet, you should already get some output from Hermes
+as it collects author information from the Git history.
+To check for this, run:
+ 
+```shell
+haggis
+```
+ 
+The output will look like follows:
+ 
+```
+Metadata harvesting
+Metadata processing
+```
+ 
+Not much to see here yet.
+You can see that there are only two stages of the pipeline executed.
+This is the default behavior as you certainly want to review the results,
+especially if you just started adding metadata to your repository.
+ 
+If you look at the output folder, you should notice a new directory `.hermes`.
+This is automatically created and maintained by Hermes to store the metadata at the different stages.
+Inside that folder you will find a sub-folder for every stage.
+The cache files are JSON and can be inspected to investigate into the results of the different stages
+(topic of future tutorial).
+ 
+```{todo}
+Write more about the different output files Hermes generates:
+ 
+- .hermes/harvest/*.json -> Harvest cache files (might be ambiguous; contains all tags)
+- .hermes/process/tags.json -> Tags for all entries in the `codemeta.json`
+- hermes.log -> Complete log file; useful for debugging
+- hermes-report.{md,html} -> Report on what Hermes did
+```
+ 
+## Configure your .gitignore
+ 
+As the `.hermes` folder contains transient caches, it is a good idea to not store it in your Git repository.
+Hence, it is a good idea to add this folder to your `.gitignore` file.
+ 
+Create a new `.gitignore` and add `/.hermes` to it:
+ 
+```
+echo "/.hermes" > .gitignore
+```
+ 
+## Provide additional metadata using CITATION.cff
+ 
+Until now, there is not much metadata to publish.
+We will change this by adding a `CITATION.cff` file to the repository.
+This file stores metadata about the authors of a software project and how to reference it in publications.
+ 
+Create a file `CITATION.cff` with the following contents:
+ 
+```yaml
+# This CITATION.cff file was generated with cffinit.
+# Visit https://bit.ly/cffinit to generate yours today!
+ 
+cff-version: 1.2.0
+title: Hermes Example Project
+message: >-
+  If you use this software, please cite it using the
+  metadata from this file.
+type: software
+authors:
+  - given-names: Michael
+    family-names: Meinel
+    email: michael.meinel@dlr.de
+    affiliation: German Aerospace Center (DLR)
+    orcid: 'https://orcid.org/0000-0001-6372-3853'
+```
+ 
+Now, if you run Hermes again, you should get some first results:
+ 
+```shell
+haggis
+```
+ 
+The output should look like the following:
+ 
+```
+Metadata harvesting
+Found valid Citation File Format file at: CITATION.cff
+Metadata processing
+```
+ 
+There is also a `codemeta.json` file generated that contains information found in `CITATION.cff`.
+You should only add `CITATION.cff` to your repository, but not the generated `codemeta.json` (at least for now).
+ 
+You will also find a `hermes-report.md` file and an matching `hermes-report.html`
+that can be reviewed to see details on what Hermes did.
+ 
+## Configuration of your project
+ 
+Hermes currently is very focussed on Python projects.
+Hence, it loads configuration settings from the `pyproject.toml` file.
+This will change in future to be more flexible.
+ 
+Until then, you can still use the `pyproject.toml` for your Hermes configuration.
+The table `tool.hermes.logging` is directly passed to Python's `logging.config.dictConfig`
+method and is used to adapt your logging output.
+ 
+Hermes currently uses the following top-level loggers:
+ 
+`cli`
+:   The log can be used to output only to command line.
+ 
+`audit`
+:   Logs to `audit.md` and should contain all processes run and (automated) decisions made.
+ 
+`audit.hints`
+:   Hints on how to resolve conflicts / ambiguities found during havest and process.
+ 
+`hermes`
+:   General logging output.
\ No newline at end of file

From c41e64fb416d9a3c01ad4c14901b516bd9e19e92 Mon Sep 17 00:00:00 2001
From: Oliver Bertuch <o.bertuch@fz-juelich.de>
Date: Mon, 20 Feb 2023 17:16:53 +0100
Subject: [PATCH 02/21] doc(tut): adapt first tutorial to latest developments

---
 .../tutorials/001-prepare-your-project.md     | 348 ++++++++++++------
 1 file changed, 245 insertions(+), 103 deletions(-)

diff --git a/docs/source/tutorials/001-prepare-your-project.md b/docs/source/tutorials/001-prepare-your-project.md
index 4c1b2732..e9421139 100644
--- a/docs/source/tutorials/001-prepare-your-project.md
+++ b/docs/source/tutorials/001-prepare-your-project.md
@@ -1,149 +1,291 @@
 <!--
-SPDX-FileCopyrightText: 2022 German Aerospace Center (DLR)
+SPDX-FileCopyrightText: 2023 German Aerospace Center (DLR), Forschungszentrum Jülich GmbH
 
 SPDX-License-Identifier: CC-BY-SA-4.0
 -->
 
 <!-- 
+SPDX-FileContributor: Oliver Bertuch
 SPDX-FileContributor: Michael Meinel
 -->
 
-# Tutorial 1: Make your project compatible with Hermes
+# T01: Add HERMES to your project
  
 In this tutorial we will guide you through the process of preparing your project for metadata publication.
-We assume that you have a project that is stored in a Git repository.
-There is no obvious additional metadata available.
+
+```{note}
+We assume that you have a project that is stored in a Git code repository on GitHub.
+```
  
-We use https://github.com/hermes-hmc/base-example throughout this tutorial.
-It should be easily adoptable to other repositories.
+We use the [HERMES showcase repo](https://github.com/hermes-hmc/showcase) throughout this tutorial.
+It should be easily adoptable to other code repositories.
  
-## Clone the repository
+## Clone the example code repository
  
-This step is optional if you use a checked-out version of your own repository.
+This step is optional if you use a checked-out version of your own code repository.
  
-```
-git clone https://github.com/hermes-hmc/base-example.git
-cd base-example
+```shell
+git clone https://github.com/hermes-hmc/showcase.git hermes-showcase
+cd hermes-showcase
 ```
  
 Your directory should look like the following:
  
-...
+```{code-block}
+---
+linenos: True
+---
+.
+├── CITATION.cff
+├── .github
+│   └── workflows
+│       └── hermes.yml
+├── .gitignore
+├── hermes.toml
+├── LICENSE
+├── pyproject.toml
+├── README.md
+└── src
+    └── showcase
+        ├── hello.py
+        └── __init__.py
+```
+
+(Again: if you use this for your own project, your mileage will vary.)
+
+At this point, the important files for HERMES are `CITATION.cff` (structured metadata), `hermes.toml`
+(workflow configuration) and `.github/workflows/hermes.yml` (CI job for publication).
  
 ## Test-drive hermes
  
-Even though there is no metadata stored yet, you should already get some output from Hermes
-as it collects author information from the Git history.
-To check for this, run:
- 
+You can run the workflow locally to verify results before adding it to your continuous integration configuration.
+
+Installation assumes you have `python` v3.10+ installed:
+
 ```shell
-haggis
+pip install "git+https://github.com/hermes-hmc/workflow.git@deRSE23"
 ```
- 
-The output will look like follows:
- 
+
+Once installed, simply run the workflow:
+
+```shell
+hermes
 ```
-Metadata harvesting
-Metadata processing
+
+The output will look like follows, indicating metadata is collated from `CITATION.cff` and `Git` history:
+
+```plain
+hermes workflow (0.1.0)
+=======================
+
+Workflow to publish research software with rich metadata
+
+# Running Hermes
+Running Hermes command line in: <some place you checked out the showcase>/hermes-showcase
+# Metadata harvesting
+- Running harvester cff
+
+## Citation File Format
+
+- Running harvester git
+
+## Git History
+
+
+# Metadata processing
+## Process data from cff
+
+### Add author names
+
+## Process data from git
+
+### Add git authors and committers as contributors
+
+### Add git branch
 ```
+
+You can see that there are only two stages of the pipeline executed, "harvesting" and "processing".
+This is the default behavior as you certainly want to review the results, especially if you just started
+adding metadata to your code repository.
  
-Not much to see here yet.
-You can see that there are only two stages of the pipeline executed.
-This is the default behavior as you certainly want to review the results,
-especially if you just started adding metadata to your repository.
- 
-If you look at the output folder, you should notice a new directory `.hermes`.
-This is automatically created and maintained by Hermes to store the metadata at the different stages.
-Inside that folder you will find a sub-folder for every stage.
-The cache files are JSON and can be inspected to investigate into the results of the different stages
-(topic of future tutorial).
- 
-```{todo}
-Write more about the different output files Hermes generates:
- 
-- .hermes/harvest/*.json -> Harvest cache files (might be ambiguous; contains all tags)
-- .hermes/process/tags.json -> Tags for all entries in the `codemeta.json`
-- hermes.log -> Complete log file; useful for debugging
-- hermes-report.{md,html} -> Report on what Hermes did
+If you look at your working directory, it should look similar to this:
+
+```{code-block}
+---
+linenos: True
+---
+.
+├── .github
+│   └── workflows
+│       └── hermes.yml
+├── .gitignore
+├── .hermes
+│   ├── harvest
+│   │   ├── cff.json
+│   │   └── git.json
+│   └── process
+│       ├── codemeta.json
+│       └── tags.json
+├── hermes-audit.md
+├── hermes.log
+├── hermes.toml
+├── LICENSE
+├── pyproject.toml
+├── README.md
+└── src
+    └── showcase
+        ├── hello.py
+        └── __init__.py
 ```
- 
+
+Note the new directory `.hermes`. This is automatically created and maintained by the workflow to store the metadata
+at the different stages. Inside that folder you will find a sub-folder for every stage.
+The cache files are JSON and can be inspected to investigate into the results of the different stages.
+
+Also new are the files `hermes-audit.md` and `hermes.log`. You may ignore both for now, they currently are mostly
+useful for development and debugging.
+
+
 ## Configure your .gitignore
  
-As the `.hermes` folder contains transient caches, it is a good idea to not store it in your Git repository.
-Hence, it is a good idea to add this folder to your `.gitignore` file.
+As the `.hermes` folder contains transient caches, it is a good idea to not store it in your code repository.
+Hence, it is a good idea to add this folder to your `.gitignore` file, along with the log files.
  
-Create a new `.gitignore` and add `/.hermes` to it:
+Create a new `.gitignore` and add `.hermes` to it:
  
 ```
-echo "/.hermes" > .gitignore
+echo ".hermes" >> .gitignore
+echo "hermes.log" >> .gitignore
+echo "hermes-audit.md" >> .gitignore
 ```
+
+(This has already been done in the `showcase` project)
  
 ## Provide additional metadata using CITATION.cff
  
-Until now, there is not much metadata to publish.
-We will change this by adding a `CITATION.cff` file to the repository.
+Until now, there is not much metadata to publish for your project.
+We will change this by adding a [`CITATION.cff`](https://citation-file-format.github.io/) file to your code repository.
 This file stores metadata about the authors of a software project and how to reference it in publications.
+
+The `showcase` project contains a fake but working example as outlined above.
+You may copy [this example file](https://github.com/hermes-hmc/showcase/blob/main/CITATION.cff) to your own project 
+and adapt or use [cffinit](https://citation-file-format.github.io/cff-initializer-javascript/) to start anew.
  
-Create a file `CITATION.cff` with the following contents:
+Please make sure to add your own `CITATION.cff` to your version controlled project.
  
-```yaml
-# This CITATION.cff file was generated with cffinit.
-# Visit https://bit.ly/cffinit to generate yours today!
+## Configuration of your project
  
-cff-version: 1.2.0
-title: Hermes Example Project
-message: >-
-  If you use this software, please cite it using the
-  metadata from this file.
-type: software
-authors:
-  - given-names: Michael
-    family-names: Meinel
-    email: michael.meinel@dlr.de
-    affiliation: German Aerospace Center (DLR)
-    orcid: 'https://orcid.org/0000-0001-6372-3853'
+The HERMES workflow is fully configurable via a [TOML](https://toml.io) file `hermes.toml`.
+This file is structured by having a table for each step of the workflow:
+
+```toml
+[harvest]
+[process]
+[deposit]
+[postprocess]
 ```
- 
-Now, if you run Hermes again, you should get some first results:
- 
+
+HERMES has opinionated defaults, living the "convention over configuration" paradigm, for every step.
+If you are not satisfied with the defaults, you can override anything by applying your own configuration.
+
+The `showcase` repository contains a `hermes.toml`, which as an example
+
+- configures to include the Git and Citation File Format metadata harvesters only,
+- disables validation in the CFF file harvester,
+- activates mapping and deposition to an Invenio based repository,
+- and configures the Zenodo Sandbox as the target publication repository:
+
+```toml
+[harvest]
+from = [ "cff", "git" ]
+
+[harvest.cff]
+validate = false
+
+[deposit]
+mapping = "invenio"
+target = "invenio"
+
+[deposit.invenio]
+base_url = "https://sandbox.zenodo.org"
+```
+
+Simply copy and paste this file to your own project for now just to get started.
+
+```{note}
+Right now, the HERMES workflow only supports a limited number of operations in its "Proof Of Concept" state.
+Expect a bumpy ride when trying to alter this minimal configuration.
+```
+
+## Optional: Testing depositing locally
+
+Targeting the Zenodo Sandbox, please [receive a "Personal Access Token" from them via your user profile](https://sandbox.zenodo.org/account/settings/applications/tokens/new/)
+with the scopes `deposit:actions` and `deposit:write` so the workflow can act on your behalf.
+
+Before executing a deposition, please think about whether you want to include your software as an artifact in it.
+A simple example to do that is to create a ZIP file of your sources, here using the `showcase` project:
+
 ```shell
-haggis
+git archive --format zip HEAD src > showcase.zip
 ```
- 
-The output should look like the following:
- 
+
+To create a software publication that also includes the software artifact now run:
+
+```shell
+hermes deposit --auth-token <PAT here> --file README.md --file showcase.zip
 ```
-Metadata harvesting
-Found valid Citation File Format file at: CITATION.cff
-Metadata processing
+
+If all goes well, you will find the URL of the deposit in the output:
+```plain
+hermes workflow (0.1.0)
+=======================
+
+Workflow to publish research software with rich metadata
+
+# Running Hermes
+Running Hermes command line in: <some place you checked out the showcase>/hermes-showcase
+Metadata deposition
+Published record: https://sandbox.zenodo.org/record/1166086
 ```
- 
-There is also a `codemeta.json` file generated that contains information found in `CITATION.cff`.
-You should only add `CITATION.cff` to your repository, but not the generated `codemeta.json` (at least for now).
- 
-You will also find a `hermes-report.md` file and an matching `hermes-report.html`
-that can be reviewed to see details on what Hermes did.
- 
-## Configuration of your project
- 
-Hermes currently is very focussed on Python projects.
-Hence, it loads configuration settings from the `pyproject.toml` file.
-This will change in future to be more flexible.
- 
-Until then, you can still use the `pyproject.toml` for your Hermes configuration.
-The table `tool.hermes.logging` is directly passed to Python's `logging.config.dictConfig`
-method and is used to adapt your logging output.
- 
-Hermes currently uses the following top-level loggers:
- 
-`cli`
-:   The log can be used to output only to command line.
- 
-`audit`
-:   Logs to `audit.md` and should contain all processes run and (automated) decisions made.
- 
-`audit.hints`
-:   Hints on how to resolve conflicts / ambiguities found during havest and process.
- 
-`hermes`
-:   General logging output.
\ No newline at end of file
+
+## Add a deposit job via CI
+
+```{note}
+This example uses Github Action syntax, but can be transfered to Jenkins or GitLab CI syntax.
+```
+
+Add a file `.github/workflows/hermes.yaml` to your project by copy and pasting
+[the example from the `showcase` project](https://github.com/hermes-hmc/showcase/blob/main/.github/workflows/hermes.yml):
+
+```yaml
+name: Software Publication
+
+on:
+  tags: # Change as you see fit for your project!
+
+jobs:
+  hermes:
+    name: HERMES
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read # We will only read content from the repo
+      # pull-requests: write # Postprocessing should be able to create a pull request with changes
+    steps:
+      - uses: actions/checkout@v2
+      - uses: actions/setup-python@v4
+        with:
+          python-version: '3.10'
+      - run: pip install git+https://github.com/hermes-hmc/workflow.git@deRSE23
+      - run: git archive --format zip HEAD src > showcase.zip
+      - run: hermes
+      - run: hermes deposit --auth-token ${{ secrets.ZENODO_SANDBOX }} --file showcase.zip --file README.md
+      # - run: hermes postprocess # (Not implemented yet)
+      # - uses: peter-evans/create-pull-request@v4 (TODO once postprocessing has it)
+```
+
+Within this workflow, we use a secret called `ZENODO_SANBOX`, which you will need to
+[add to your Github repository](https://docs.github.com/en/actions/security-guides/encrypted-secrets#creating-encrypted-secrets-for-a-repository)
+and contains your "Personal Access Token".
+
+Now, once you create a new Git tag in your code repository, the HERMES workflow will create a rich metadata
+software publication for you within the Zenodo Sandbox.

From a52a809092422d7a46f17f187f107aa325c2063f Mon Sep 17 00:00:00 2001
From: Oliver Bertuch <o.bertuch@fz-juelich.de>
Date: Mon, 20 Feb 2023 17:22:47 +0100
Subject: [PATCH 03/21] fix,docs(tut): change to correct pygement lexer

---
 docs/source/tutorials/001-prepare-your-project.md | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/docs/source/tutorials/001-prepare-your-project.md b/docs/source/tutorials/001-prepare-your-project.md
index e9421139..dcdce966 100644
--- a/docs/source/tutorials/001-prepare-your-project.md
+++ b/docs/source/tutorials/001-prepare-your-project.md
@@ -74,7 +74,7 @@ hermes
 
 The output will look like follows, indicating metadata is collated from `CITATION.cff` and `Git` history:
 
-```plain
+```text
 hermes workflow (0.1.0)
 =======================
 
@@ -236,7 +236,7 @@ hermes deposit --auth-token <PAT here> --file README.md --file showcase.zip
 ```
 
 If all goes well, you will find the URL of the deposit in the output:
-```plain
+```text
 hermes workflow (0.1.0)
 =======================
 

From 6d3297504a2eff33e5d29e19de07e87c5fec04a0 Mon Sep 17 00:00:00 2001
From: Oliver Bertuch <o.bertuch@fz-juelich.de>
Date: Wed, 17 May 2023 13:41:48 +0200
Subject: [PATCH 04/21] docs: add Sphinx Click extension

---
 docs/source/conf.py | 1 +
 pyproject.toml      | 1 +
 2 files changed, 2 insertions(+)

diff --git a/docs/source/conf.py b/docs/source/conf.py
index 1c7a0103..3abed1be 100644
--- a/docs/source/conf.py
+++ b/docs/source/conf.py
@@ -55,6 +55,7 @@
     "sphinxext.opengraph",
     'myst_parser',
     'autoapi.extension',
+    'sphinx_click',
 ]
 
 language = 'en'
diff --git a/pyproject.toml b/pyproject.toml
index cd95f3bf..247d8b73 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -66,6 +66,7 @@ sphinx-autobuild = "^2021.3.14"
 sphinx-autoapi = "^2.0.0"
 sphinxemoji = "^0.2.0"
 sphinxext-opengraph = "^0.6.3"
+sphinx-click = "^4.4.0"
 reuse = "^1.0.0"
 
 [tool.poetry.plugins.console_scripts]

From 1dcd652c292fed8927a05bae2ff204c3cec7abc0 Mon Sep 17 00:00:00 2001
From: Oliver Bertuch <o.bertuch@fz-juelich.de>
Date: Wed, 17 May 2023 13:42:14 +0200
Subject: [PATCH 05/21] docs: add initial CLI usage help page

---
 docs/source/cli.rst  | 16 ++++++++++++++++
 docs/source/index.md |  4 ++++
 2 files changed, 20 insertions(+)
 create mode 100644 docs/source/cli.rst

diff --git a/docs/source/cli.rst b/docs/source/cli.rst
new file mode 100644
index 00000000..fd032c8a
--- /dev/null
+++ b/docs/source/cli.rst
@@ -0,0 +1,16 @@
+..
+    SPDX-FileCopyrightText: 2023 Forschungszentrum Jülich
+    SPDX-License-Identifier: CC-BY-SA-4.0
+    SPDX-FileContributor: Oliver Bertuch
+
+..
+    This page must use reStructuredText rather than Markdown to enable parsing and formating the rst-based
+    output of the sphinx-click plugin.
+
+CLI Usage
+=========
+
+.. click:: hermes.cli:main
+  :prog: hermes
+  :nested: full
+
diff --git a/docs/source/index.md b/docs/source/index.md
index 6bfe7b9b..0d6e6e17 100644
--- a/docs/source/index.md
+++ b/docs/source/index.md
@@ -42,6 +42,10 @@ automatic submission to publication repositories.
 tutorials/*
 ```
 
+```{toctree}
+cli
+```
+
 ```{toctree}
 :maxdepth: 1
 :caption: Developers

From 8e6cbb463ef5b6f427b1816e9467aba1b5b168fb Mon Sep 17 00:00:00 2001
From: Oliver Bertuch <o.bertuch@fz-juelich.de>
Date: Wed, 17 May 2023 13:43:54 +0200
Subject: [PATCH 06/21] docs: correction of repository button URL

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

diff --git a/docs/source/conf.py b/docs/source/conf.py
index 3abed1be..c7464f9c 100644
--- a/docs/source/conf.py
+++ b/docs/source/conf.py
@@ -116,7 +116,7 @@
                     target='_blank'>Helmholtz Association</a> in the framework of the \
                     <a href='https://helmholtz-metadaten.de' targe='_blank'>Helmholtz Metadata \
                     Collaboration</a></div>",
-    "repository_url": "https://github.com/hermes-hmc/project",
+    "repository_url": "https://github.com/hermes-hmc/workflow",
     "use_repository_button": True,
 }
 

From 15e9dd89307f5c4c81f6ba4a28460937c0de7bbd Mon Sep 17 00:00:00 2001
From: Oliver Bertuch <o.bertuch@fz-juelich.de>
Date: Wed, 17 May 2023 13:45:21 +0200
Subject: [PATCH 07/21] chore: update poetry.lock after adding sphinx-click

---
 poetry.lock | 1545 ++++++++++++++++++++++++++-------------------------
 1 file changed, 783 insertions(+), 762 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index cf7aa99e..961858b4 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1,3 +1,5 @@
+# This file is automatically @generated by Poetry 1.4.2 and should not be changed by hand.
+
 [[package]]
 name = "alabaster"
 version = "0.7.13"
@@ -5,6 +7,10 @@ description = "A configurable sidebar-enabled Sphinx theme"
 category = "dev"
 optional = false
 python-versions = ">=3.6"
+files = [
+    {file = "alabaster-0.7.13-py3-none-any.whl", hash = "sha256:1ee19aca801bbabb5ba3f5f258e4422dfa86f82f3e9cefb0859b283cdd7f62a3"},
+    {file = "alabaster-0.7.13.tar.gz", hash = "sha256:a27a4a084d5e690e16e01e03ad2b2e552c61a65469419b907243193de1a84ae2"},
+]
 
 [[package]]
 name = "astroid"
@@ -13,6 +19,10 @@ description = "An abstract syntax tree for Python with inference support."
 category = "dev"
 optional = false
 python-versions = ">=3.7.2"
+files = [
+    {file = "astroid-2.15.0-py3-none-any.whl", hash = "sha256:e3e4d0ffc2d15d954065579689c36aac57a339a4679a679579af6401db4d3fdb"},
+    {file = "astroid-2.15.0.tar.gz", hash = "sha256:525f126d5dc1b8b0b6ee398b33159105615d92dc4a17f2cd064125d57f6186fa"},
+]
 
 [package.dependencies]
 lazy-object-proxy = ">=1.4.0"
@@ -29,6 +39,10 @@ description = "Classes Without Boilerplate"
 category = "main"
 optional = false
 python-versions = ">=3.6"
+files = [
+    {file = "attrs-22.2.0-py3-none-any.whl", hash = "sha256:29e95c7f6778868dbd49170f98f8818f78f3dc5e0e37c0b1f474e3561b240836"},
+    {file = "attrs-22.2.0.tar.gz", hash = "sha256:c9227bfc2f01993c03f68db37d1d15c9690188323c067c641f1a35ca58185f99"},
+]
 
 [package.extras]
 cov = ["attrs[tests]", "coverage-enable-subprocess", "coverage[toml] (>=5.3)"]
@@ -44,6 +58,10 @@ description = "Internationalization utilities"
 category = "dev"
 optional = false
 python-versions = ">=3.7"
+files = [
+    {file = "Babel-2.12.1-py3-none-any.whl", hash = "sha256:b4246fb7677d3b98f501a39d43396d3cafdc8eadb045f4a31be01863f655c610"},
+    {file = "Babel-2.12.1.tar.gz", hash = "sha256:cc2d99999cd01d44420ae725a21c9e3711b3aadc7976d6147f622d8581963455"},
+]
 
 [[package]]
 name = "beautifulsoup4"
@@ -52,6 +70,10 @@ description = "Screen-scraping library"
 category = "dev"
 optional = false
 python-versions = ">=3.6.0"
+files = [
+    {file = "beautifulsoup4-4.12.0-py3-none-any.whl", hash = "sha256:2130a5ad7f513200fae61a17abb5e338ca980fa28c439c0571014bc0217e9591"},
+    {file = "beautifulsoup4-4.12.0.tar.gz", hash = "sha256:c5fceeaec29d09c84970e47c65f2f0efe57872f7cff494c9691a26ec0ff13234"},
+]
 
 [package.dependencies]
 soupsieve = ">1.2"
@@ -67,6 +89,10 @@ description = "Ultra-lightweight pure Python package to check if a file is binar
 category = "dev"
 optional = false
 python-versions = "*"
+files = [
+    {file = "binaryornot-0.4.4-py2.py3-none-any.whl", hash = "sha256:b8b71173c917bddcd2c16070412e369c3ed7f0528926f70cac18a6c97fd563e4"},
+    {file = "binaryornot-0.4.4.tar.gz", hash = "sha256:359501dfc9d40632edc9fac890e19542db1a287bbcfa58175b66658392018061"},
+]
 
 [package.dependencies]
 chardet = ">=3.0.2"
@@ -78,6 +104,10 @@ description = "Define boolean algebras, create and parse boolean expressions and
 category = "dev"
 optional = false
 python-versions = "*"
+files = [
+    {file = "boolean.py-4.0-py3-none-any.whl", hash = "sha256:2876f2051d7d6394a531d82dc6eb407faa0b01a0a0b3083817ccd7323b8d96bd"},
+    {file = "boolean.py-4.0.tar.gz", hash = "sha256:17b9a181630e43dde1851d42bef546d616d5d9b4480357514597e78b203d06e4"},
+]
 
 [[package]]
 name = "certifi"
@@ -86,6 +116,10 @@ description = "Python package for providing Mozilla's CA Bundle."
 category = "main"
 optional = false
 python-versions = ">=3.6"
+files = [
+    {file = "certifi-2022.12.7-py3-none-any.whl", hash = "sha256:4ad3232f5e926d6718ec31cfc1fcadfde020920e278684144551c91769c7bc18"},
+    {file = "certifi-2022.12.7.tar.gz", hash = "sha256:35824b4c3a97115964b408844d64aa14db1cc518f6562e8d7261699d1350a9e3"},
+]
 
 [[package]]
 name = "cffconvert"
@@ -94,6 +128,7 @@ description = ""
 category = "main"
 optional = false
 python-versions = "*"
+files = []
 develop = false
 
 [package.dependencies]
@@ -121,6 +156,10 @@ description = "Universal encoding detector for Python 3"
 category = "dev"
 optional = false
 python-versions = ">=3.7"
+files = [
+    {file = "chardet-5.1.0-py3-none-any.whl", hash = "sha256:362777fb014af596ad31334fde1e8c327dfdb076e1960d1694662d46a6917ab9"},
+    {file = "chardet-5.1.0.tar.gz", hash = "sha256:0d62712b956bc154f85fb0a266e2a3c5913c2967e00348701b32411d6def31e5"},
+]
 
 [[package]]
 name = "charset-normalizer"
@@ -129,6 +168,83 @@ description = "The Real First Universal Charset Detector. Open, modern and activ
 category = "main"
 optional = false
 python-versions = ">=3.7.0"
+files = [
+    {file = "charset-normalizer-3.1.0.tar.gz", hash = "sha256:34e0a2f9c370eb95597aae63bf85eb5e96826d81e3dcf88b8886012906f509b5"},
+    {file = "charset_normalizer-3.1.0-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:e0ac8959c929593fee38da1c2b64ee9778733cdf03c482c9ff1d508b6b593b2b"},
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+]
 
 [[package]]
 name = "click"
@@ -137,6 +253,10 @@ description = "Composable command line interface toolkit"
 category = "main"
 optional = false
 python-versions = ">=3.7"
+files = [
+    {file = "click-8.1.3-py3-none-any.whl", hash = "sha256:bb4d8133cb15a609f44e8213d9b391b0809795062913b383c62be0ee95b1db48"},
+    {file = "click-8.1.3.tar.gz", hash = "sha256:7682dc8afb30297001674575ea00d1814d808d6a36af415a82bd481d37ba7b8e"},
+]
 
 [package.dependencies]
 colorama = {version = "*", markers = "platform_system == \"Windows\""}
@@ -148,6 +268,10 @@ description = "Cross-platform colored terminal text."
 category = "main"
 optional = false
 python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,!=3.6.*,>=2.7"
+files = [
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+]
 
 [[package]]
 name = "convert-codemeta"
@@ -156,6 +280,10 @@ description = "Convert and validate codemeta."
 category = "main"
 optional = false
 python-versions = "*"
+files = [
+    {file = "convert_codemeta-0.4.0-py3-none-any.whl", hash = "sha256:9b7a52ca55e0319cade40084401a1a7431ecb6fecdd73950a92be66ab7bb4b38"},
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+]
 
 [package.dependencies]
 pandas = ">=1.0.0"
@@ -172,6 +300,59 @@ description = "Code coverage measurement for Python"
 category = "dev"
 optional = false
 python-versions = ">=3.7"
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+    {file = "coverage-7.2.2-pp37.pp38.pp39-none-any.whl", hash = "sha256:872d6ce1f5be73f05bea4df498c140b9e7ee5418bfa2cc8204e7f9b817caa968"},
+    {file = "coverage-7.2.2.tar.gz", hash = "sha256:36dd42da34fe94ed98c39887b86db9d06777b1c8f860520e21126a75507024f2"},
+]
 
 [package.dependencies]
 tomli = {version = "*", optional = true, markers = "python_full_version <= \"3.11.0a6\" and extra == \"toml\""}
@@ -186,6 +367,10 @@ description = "Python @deprecated decorator to deprecate old python classes, fun
 category = "dev"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
+files = [
+    {file = "Deprecated-1.2.13-py2.py3-none-any.whl", hash = "sha256:64756e3e14c8c5eea9795d93c524551432a0be75629f8f29e67ab8caf076c76d"},
+    {file = "Deprecated-1.2.13.tar.gz", hash = "sha256:43ac5335da90c31c24ba028af536a91d41d53f9e6901ddb021bcc572ce44e38d"},
+]
 
 [package.dependencies]
 wrapt = ">=1.10,<2"
@@ -200,6 +385,9 @@ description = "Pythonic argument parser, that will make you smile"
 category = "main"
 optional = false
 python-versions = "*"
+files = [
+    {file = "docopt-0.6.2.tar.gz", hash = "sha256:49b3a825280bd66b3aa83585ef59c4a8c82f2c8a522dbe754a8bc8d08c85c491"},
+]
 
 [[package]]
 name = "docutils"
@@ -208,6 +396,10 @@ description = "Docutils -- Python Documentation Utilities"
 category = "dev"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
+files = [
+    {file = "docutils-0.17.1-py2.py3-none-any.whl", hash = "sha256:cf316c8370a737a022b72b56874f6602acf974a37a9fba42ec2876387549fc61"},
+    {file = "docutils-0.17.1.tar.gz", hash = "sha256:686577d2e4c32380bb50cbb22f575ed742d58168cee37e99117a854bcd88f125"},
+]
 
 [[package]]
 name = "exceptiongroup"
@@ -216,6 +408,10 @@ description = "Backport of PEP 654 (exception groups)"
 category = "dev"
 optional = false
 python-versions = ">=3.7"
+files = [
+    {file = "exceptiongroup-1.1.1-py3-none-any.whl", hash = "sha256:232c37c63e4f682982c8b6459f33a8981039e5fb8756b2074364e5055c498c9e"},
+    {file = "exceptiongroup-1.1.1.tar.gz", hash = "sha256:d484c3090ba2889ae2928419117447a14daf3c1231d5e30d0aae34f354f01785"},
+]
 
 [package.extras]
 test = ["pytest (>=6)"]
@@ -227,6 +423,10 @@ description = "the modular source code checker: pep8 pyflakes and co"
 category = "dev"
 optional = false
 python-versions = ">=3.6.1"
+files = [
+    {file = "flake8-5.0.4-py2.py3-none-any.whl", hash = "sha256:7a1cf6b73744f5806ab95e526f6f0d8c01c66d7bbe349562d22dfca20610b248"},
+    {file = "flake8-5.0.4.tar.gz", hash = "sha256:6fbe320aad8d6b95cec8b8e47bc933004678dc63095be98528b7bdd2a9f510db"},
+]
 
 [package.dependencies]
 mccabe = ">=0.7.0,<0.8.0"
@@ -240,6 +440,10 @@ description = "Internationalized Domain Names in Applications (IDNA)"
 category = "main"
 optional = false
 python-versions = ">=3.5"
+files = [
+    {file = "idna-3.4-py3-none-any.whl", hash = "sha256:90b77e79eaa3eba6de819a0c442c0b4ceefc341a7a2ab77d7562bf49f425c5c2"},
+    {file = "idna-3.4.tar.gz", hash = "sha256:814f528e8dead7d329833b91c5faa87d60bf71824cd12a7530b5526063d02cb4"},
+]
 
 [[package]]
 name = "imagesize"
@@ -248,6 +452,10 @@ description = "Getting image size from png/jpeg/jpeg2000/gif file"
 category = "dev"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
+files = [
+    {file = "imagesize-1.4.1-py2.py3-none-any.whl", hash = "sha256:0d8d18d08f840c19d0ee7ca1fd82490fdc3729b7ac93f49870406ddde8ef8d8b"},
+    {file = "imagesize-1.4.1.tar.gz", hash = "sha256:69150444affb9cb0d5cc5a92b3676f0b2fb7cd9ae39e947a5e11a36b4497cd4a"},
+]
 
 [[package]]
 name = "iniconfig"
@@ -256,6 +464,10 @@ description = "brain-dead simple config-ini parsing"
 category = "dev"
 optional = false
 python-versions = ">=3.7"
+files = [
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+    {file = "iniconfig-2.0.0.tar.gz", hash = "sha256:2d91e135bf72d31a410b17c16da610a82cb55f6b0477d1a902134b24a455b8b3"},
+]
 
 [[package]]
 name = "jinja2"
@@ -264,6 +476,10 @@ description = "A very fast and expressive template engine."
 category = "dev"
 optional = false
 python-versions = ">=3.7"
+files = [
+    {file = "Jinja2-3.1.2-py3-none-any.whl", hash = "sha256:6088930bfe239f0e6710546ab9c19c9ef35e29792895fed6e6e31a023a182a61"},
+    {file = "Jinja2-3.1.2.tar.gz", hash = "sha256:31351a702a408a9e7595a8fc6150fc3f43bb6bf7e319770cbc0db9df9437e852"},
+]
 
 [package.dependencies]
 MarkupSafe = ">=2.0"
@@ -278,6 +494,10 @@ description = "An implementation of JSON Schema validation for Python"
 category = "main"
 optional = false
 python-versions = "*"
+files = [
+    {file = "jsonschema-3.2.0-py2.py3-none-any.whl", hash = "sha256:4e5b3cf8216f577bee9ce139cbe72eca3ea4f292ec60928ff24758ce626cd163"},
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+]
 
 [package.dependencies]
 attrs = ">=17.4.0"
@@ -296,6 +516,44 @@ description = "A fast and thorough lazy object proxy."
 category = "dev"
 optional = false
 python-versions = ">=3.7"
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+]
 
 [[package]]
 name = "license-expression"
@@ -304,6 +562,10 @@ description = "license-expression is a comprehensive utility library to parse, c
 category = "dev"
 optional = false
 python-versions = ">=3.7"
+files = [
+    {file = "license-expression-30.1.0.tar.gz", hash = "sha256:943b1d2cde251bd30a166b509f78990fdd060be9750f3f1a324571e804857a53"},
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+]
 
 [package.dependencies]
 "boolean.py" = ">=4.0"
@@ -319,6 +581,10 @@ description = "Python LiveReload is an awesome tool for web developers"
 category = "dev"
 optional = false
 python-versions = "*"
+files = [
+    {file = "livereload-2.6.3-py2.py3-none-any.whl", hash = "sha256:ad4ac6f53b2d62bb6ce1a5e6e96f1f00976a32348afedcb4b6d68df2a1d346e4"},
+    {file = "livereload-2.6.3.tar.gz", hash = "sha256:776f2f865e59fde56490a56bcc6773b6917366bce0c267c60ee8aaf1a0959869"},
+]
 
 [package.dependencies]
 six = "*"
@@ -331,6 +597,10 @@ description = "Python port of markdown-it. Markdown parsing, done right!"
 category = "dev"
 optional = false
 python-versions = ">=3.7"
+files = [
+    {file = "markdown-it-py-2.2.0.tar.gz", hash = "sha256:7c9a5e412688bc771c67432cbfebcdd686c93ce6484913dccf06cb5a0bea35a1"},
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+]
 
 [package.dependencies]
 mdurl = ">=0.1,<1.0"
@@ -352,23 +622,83 @@ description = "Safely add untrusted strings to HTML/XML markup."
 category = "dev"
 optional = false
 python-versions = ">=3.7"
-
-[[package]]
-name = "mccabe"
-version = "0.7.0"
-description = "McCabe checker, plugin for flake8"
-category = "dev"
-optional = false
-python-versions = ">=3.6"
-
-[[package]]
-name = "mdit-py-plugins"
-version = "0.3.5"
-description = "Collection of plugins for markdown-it-py"
-category = "dev"
-optional = false
-python-versions = ">=3.7"
-
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+description = "McCabe checker, plugin for flake8"
+category = "dev"
+optional = false
+python-versions = ">=3.6"
+files = [
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+
+[[package]]
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+version = "0.3.5"
+description = "Collection of plugins for markdown-it-py"
+category = "dev"
+optional = false
+python-versions = ">=3.7"
+files = [
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 markdown-it-py = ">=1.0.0,<3.0.0"
 
@@ -384,6 +714,10 @@ description = "Markdown URL utilities"
 category = "dev"
 optional = false
 python-versions = ">=3.7"
+files = [
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+]
 
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 name = "mslex"
@@ -392,6 +726,10 @@ description = "shlex for windows"
 category = "dev"
 optional = false
 python-versions = ">=3.5"
+files = [
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+]
 
 [[package]]
 name = "myst-parser"
@@ -400,6 +738,10 @@ description = "An extended commonmark compliant parser, with bridges to docutils
 category = "dev"
 optional = false
 python-versions = ">=3.7"
+files = [
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 [package.dependencies]
 docutils = ">=0.15,<0.20"
@@ -423,6 +765,36 @@ description = "Fundamental package for array computing in Python"
 category = "main"
 optional = false
 python-versions = ">=3.8"
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+]
 
 [[package]]
 name = "packaging"
@@ -431,6 +803,10 @@ description = "Core utilities for Python packages"
 category = "dev"
 optional = false
 python-versions = ">=3.7"
+files = [
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+]
 
 [[package]]
 name = "pandas"
@@ -439,6 +815,35 @@ description = "Powerful data structures for data analysis, time series, and stat
 category = "main"
 optional = false
 python-versions = ">=3.8"
+files = [
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 [package.dependencies]
 numpy = [
@@ -458,6 +863,10 @@ description = "plugin and hook calling mechanisms for python"
 category = "dev"
 optional = false
 python-versions = ">=3.6"
+files = [
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 [package.extras]
 dev = ["pre-commit", "tox"]
@@ -470,6 +879,22 @@ description = "Cross-platform lib for process and system monitoring in Python."
 category = "dev"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
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+]
 
 [package.extras]
 test = ["enum34", "ipaddress", "mock", "pywin32", "wmi"]
@@ -481,6 +906,10 @@ description = "Python style guide checker"
 category = "dev"
 optional = false
 python-versions = ">=3.6"
+files = [
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+]
 
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 name = "pydata-sphinx-theme"
@@ -489,6 +918,10 @@ description = "Bootstrap-based Sphinx theme from the PyData community"
 category = "dev"
 optional = false
 python-versions = ">=3.7"
+files = [
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 [package.dependencies]
 beautifulsoup4 = "*"
@@ -509,6 +942,10 @@ description = "passive checker of Python programs"
 category = "dev"
 optional = false
 python-versions = ">=3.6"
+files = [
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+]
 
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 name = "pygments"
@@ -517,6 +954,10 @@ description = "Pygments is a syntax highlighting package written in Python."
 category = "dev"
 optional = false
 python-versions = ">=3.6"
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 plugins = ["importlib-metadata"]
@@ -528,6 +969,10 @@ description = "Python lib/cli for JSON/YAML schema validation"
 category = "main"
 optional = false
 python-versions = "*"
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 docopt = ">=0.6.2"
@@ -541,6 +986,9 @@ description = "Python implementation of the JSON-LD API"
 category = "main"
 optional = false
 python-versions = "*"
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 [package.dependencies]
 requests = {version = "*", optional = true, markers = "extra == \"requests\""}
@@ -556,6 +1004,10 @@ description = "pyparsing module - Classes and methods to define and execute pars
 category = "main"
 optional = false
 python-versions = ">=3.6.8"
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 [package.extras]
 diagrams = ["jinja2", "railroad-diagrams"]
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 category = "main"
 optional = false
 python-versions = ">=3.7"
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 [[package]]
 name = "pytest"
@@ -575,6 +1056,10 @@ description = "pytest: simple powerful testing with Python"
 category = "dev"
 optional = false
 python-versions = ">=3.7"
+files = [
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+]
 
 [package.dependencies]
 attrs = ">=19.2.0"
@@ -595,6 +1080,10 @@ description = "Pytest plugin for measuring coverage."
 category = "dev"
 optional = false
 python-versions = ">=3.6"
+files = [
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 [package.dependencies]
 coverage = {version = ">=5.2.1", extras = ["toml"]}
@@ -610,6 +1099,10 @@ description = "Extensions to the standard Python datetime module"
 category = "main"
 optional = false
 python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,>=2.7"
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 [package.dependencies]
 six = ">=1.5"
@@ -621,6 +1114,10 @@ description = "Debian package related modules"
 category = "dev"
 optional = false
 python-versions = ">=3.5"
+files = [
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 [package.dependencies]
 chardet = "*"
@@ -632,6 +1129,10 @@ description = "World timezone definitions, modern and historical"
 category = "main"
 optional = false
 python-versions = "*"
+files = [
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 [[package]]
 name = "pyyaml"
@@ -640,38 +1141,88 @@ description = "YAML parser and emitter for Python"
 category = "dev"
 optional = false
 python-versions = ">=3.6"
-
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-optional = false
-python-versions = "*"
-
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-requests = ">=2.3,<3"
-six = "*"
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+]
+
+[[package]]
+name = "requests"
+version = "2.28.2"
+description = "Python HTTP for Humans."
+category = "main"
+optional = false
+python-versions = ">=3.7, <4"
+files = [
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+]
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+[package.dependencies]
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+charset-normalizer = ">=2,<4"
+idna = ">=2.5,<4"
+urllib3 = ">=1.21.1,<1.27"
+
+[package.extras]
+socks = ["PySocks (>=1.5.6,!=1.5.7)"]
+use-chardet-on-py3 = ["chardet (>=3.0.2,<6)"]
+
+[[package]]
+name = "requests-mock"
+version = "1.10.0"
+description = "Mock out responses from the requests package"
+category = "dev"
+optional = false
+python-versions = "*"
+files = [
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+]
+
+[package.dependencies]
+requests = ">=2.3,<3"
+six = "*"
+
+[package.extras]
 fixture = ["fixtures"]
 test = ["fixtures", "mock", "purl", "pytest", "requests-futures", "sphinx", "testrepository (>=0.0.18)", "testtools"]
 
@@ -682,6 +1233,10 @@ description = "reuse is a tool for compliance with the REUSE recommendations."
 category = "dev"
 optional = false
 python-versions = ">=3.6.2,<4.0.0"
+files = [
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+]
 
 [package.dependencies]
 binaryornot = ">=0.4.4,<0.5.0"
@@ -698,6 +1253,10 @@ description = "ruamel.yaml is a YAML parser/emitter that supports roundtrip pres
 category = "main"
 optional = false
 python-versions = ">=3"
+files = [
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+]
 
 [package.dependencies]
 "ruamel.yaml.clib" = {version = ">=0.2.6", markers = "platform_python_implementation == \"CPython\" and python_version < \"3.11\""}
@@ -713,6 +1272,44 @@ description = "C version of reader, parser and emitter for ruamel.yaml derived f
 category = "main"
 optional = false
 python-versions = ">=3.5"
+files = [
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+    {file = "ruamel.yaml.clib-0.2.7-cp39-cp39-win32.whl", hash = "sha256:d5e51e2901ec2366b79f16c2299a03e74ba4531ddcfacc1416639c557aef0ad8"},
+    {file = "ruamel.yaml.clib-0.2.7-cp39-cp39-win_amd64.whl", hash = "sha256:184faeaec61dbaa3cace407cffc5819f7b977e75360e8d5ca19461cd851a5fc5"},
+    {file = "ruamel.yaml.clib-0.2.7.tar.gz", hash = "sha256:1f08fd5a2bea9c4180db71678e850b995d2a5f4537be0e94557668cf0f5f9497"},
+]
 
 [[package]]
 name = "setuptools"
@@ -721,6 +1318,10 @@ description = "Easily download, build, install, upgrade, and uninstall Python pa
 category = "main"
 optional = false
 python-versions = ">=3.7"
+files = [
+    {file = "setuptools-67.6.0-py3-none-any.whl", hash = "sha256:b78aaa36f6b90a074c1fa651168723acbf45d14cb1196b6f02c0fd07f17623b2"},
+    {file = "setuptools-67.6.0.tar.gz", hash = "sha256:2ee892cd5f29f3373097f5a814697e397cf3ce313616df0af11231e2ad118077"},
+]
 
 [package.extras]
 docs = ["furo", "jaraco.packaging (>=9)", "jaraco.tidelift (>=1.4)", "pygments-github-lexers (==0.0.5)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-favicon", "sphinx-hoverxref (<2)", "sphinx-inline-tabs", "sphinx-lint", "sphinx-notfound-page (==0.8.3)", "sphinx-reredirects", "sphinxcontrib-towncrier"]
@@ -734,6 +1335,10 @@ description = "Python 2 and 3 compatibility utilities"
 category = "main"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*"
+files = [
+    {file = "six-1.16.0-py2.py3-none-any.whl", hash = "sha256:8abb2f1d86890a2dfb989f9a77cfcfd3e47c2a354b01111771326f8aa26e0254"},
+    {file = "six-1.16.0.tar.gz", hash = "sha256:1e61c37477a1626458e36f7b1d82aa5c9b094fa4802892072e49de9c60c4c926"},
+]
 
 [[package]]
 name = "snowballstemmer"
@@ -742,6 +1347,10 @@ description = "This package provides 29 stemmers for 28 languages generated from
 category = "dev"
 optional = false
 python-versions = "*"
+files = [
+    {file = "snowballstemmer-2.2.0-py2.py3-none-any.whl", hash = "sha256:c8e1716e83cc398ae16824e5572ae04e0d9fc2c6b985fb0f900f5f0c96ecba1a"},
+    {file = "snowballstemmer-2.2.0.tar.gz", hash = "sha256:09b16deb8547d3412ad7b590689584cd0fe25ec8db3be37788be3810cbf19cb1"},
+]
 
 [[package]]
 name = "soupsieve"
@@ -750,6 +1359,10 @@ description = "A modern CSS selector implementation for Beautiful Soup."
 category = "dev"
 optional = false
 python-versions = ">=3.7"
+files = [
+    {file = "soupsieve-2.4-py3-none-any.whl", hash = "sha256:49e5368c2cda80ee7e84da9dbe3e110b70a4575f196efb74e51b94549d921955"},
+    {file = "soupsieve-2.4.tar.gz", hash = "sha256:e28dba9ca6c7c00173e34e4ba57448f0688bb681b7c5e8bf4971daafc093d69a"},
+]
 
 [[package]]
 name = "sphinx"
@@ -758,6 +1371,10 @@ description = "Python documentation generator"
 category = "dev"
 optional = false
 python-versions = ">=3.6"
+files = [
+    {file = "Sphinx-4.5.0-py3-none-any.whl", hash = "sha256:ebf612653238bcc8f4359627a9b7ce44ede6fdd75d9d30f68255c7383d3a6226"},
+    {file = "Sphinx-4.5.0.tar.gz", hash = "sha256:7bf8ca9637a4ee15af412d1a1d9689fec70523a68ca9bb9127c2f3eeb344e2e6"},
+]
 
 [package.dependencies]
 alabaster = ">=0.7,<0.8"
@@ -789,6 +1406,10 @@ description = "Sphinx API documentation generator"
 category = "dev"
 optional = false
 python-versions = ">=3.7"
+files = [
+    {file = "sphinx-autoapi-2.0.1.tar.gz", hash = "sha256:cdf47968c20852f4feb0ccefd09e414bb820af8af8f82fab15a24b09a3d1baba"},
+    {file = "sphinx_autoapi-2.0.1-py2.py3-none-any.whl", hash = "sha256:8ed197a0c9108770aa442a5445744c1405b356ea64df848e8553411b9b9e129b"},
+]
 
 [package.dependencies]
 astroid = ">=2.7"
@@ -809,6 +1430,10 @@ description = "Rebuild Sphinx documentation on changes, with live-reload in the
 category = "dev"
 optional = false
 python-versions = ">=3.6"
+files = [
+    {file = "sphinx-autobuild-2021.3.14.tar.gz", hash = "sha256:de1ca3b66e271d2b5b5140c35034c89e47f263f2cd5db302c9217065f7443f05"},
+    {file = "sphinx_autobuild-2021.3.14-py3-none-any.whl", hash = "sha256:8fe8cbfdb75db04475232f05187c776f46f6e9e04cacf1e49ce81bdac649ccac"},
+]
 
 [package.dependencies]
 colorama = "*"
@@ -825,6 +1450,10 @@ description = "A clean book theme for scientific explanations and documentation
 category = "dev"
 optional = false
 python-versions = ">=3.7"
+files = [
+    {file = "sphinx_book_theme-0.3.3-py3-none-any.whl", hash = "sha256:9685959dbbb492af005165ef1b9229fdd5d5431580ac181578beae3b4d012d91"},
+    {file = "sphinx_book_theme-0.3.3.tar.gz", hash = "sha256:0ec36208ff14c6d6bf8aee1f1f8268e0c6e2bfa3cef6e41143312b25275a6217"},
+]
 
 [package.dependencies]
 pydata-sphinx-theme = ">=0.8.0,<0.9.0"
@@ -836,6 +1465,23 @@ code-style = ["pre-commit (>=2.7.0,<2.8.0)"]
 doc = ["ablog (>=0.10.13,<0.11.0)", "folium", "ipywidgets", "matplotlib", "myst-nb (>=0.13.2,<0.14.0)", "nbclient", "numpy", "numpydoc", "pandas", "plotly", "sphinx (>=4.0,<5.0)", "sphinx-copybutton", "sphinx-design", "sphinx-examples", "sphinx-tabs", "sphinx-thebe (>=0.1.1)", "sphinx-togglebutton (>=0.2.1)", "sphinxcontrib-bibtex (>=2.2,<3.0)", "sphinxcontrib-youtube", "sphinxext-opengraph"]
 test = ["beautifulsoup4 (>=4.6.1,<5)", "coverage", "myst-nb (>=0.13.2,<0.14.0)", "pytest (>=6.0.1,<6.1.0)", "pytest-cov", "pytest-regressions (>=2.0.1,<2.1.0)", "sphinx_thebe"]
 
+[[package]]
+name = "sphinx-click"
+version = "4.4.0"
+description = "Sphinx extension that automatically documents click applications"
+category = "dev"
+optional = false
+python-versions = ">=3.7"
+files = [
+    {file = "sphinx-click-4.4.0.tar.gz", hash = "sha256:cc67692bd28f482c7f01531c61b64e9d2f069bfcf3d24cbbb51d4a84a749fa48"},
+    {file = "sphinx_click-4.4.0-py3-none-any.whl", hash = "sha256:2821c10a68fc9ee6ce7c92fad26540d8d8c8f45e6d7258f0e4fb7529ae8fab49"},
+]
+
+[package.dependencies]
+click = ">=7.0"
+docutils = "*"
+sphinx = ">=2.0"
+
 [[package]]
 name = "sphinx-favicon"
 version = "0.2"
@@ -843,6 +1489,10 @@ description = "Sphinx Extension adding support for custom favicons"
 category = "dev"
 optional = false
 python-versions = ">=3.6"
+files = [
+    {file = "sphinx-favicon-0.2.tar.gz", hash = "sha256:73436a1f5f80c4fcae6eadd2520b9c2bc6c1aec0d91d153b3774359bdd103a58"},
+    {file = "sphinx_favicon-0.2-py3-none-any.whl", hash = "sha256:0b17cb0f9b97fb99172d47fb11fbdd0aadb26cbe0f6368e81843176ca18d06e6"},
+]
 
 [package.dependencies]
 sphinx = ">=3.4"
@@ -854,6 +1504,9 @@ description = "A sphinx custom role to embed inline fontawesome incon in the lat
 category = "dev"
 optional = false
 python-versions = ">=3.6.9"
+files = [
+    {file = "sphinx-icon-0.1.2.tar.gz", hash = "sha256:e4adc9922e2e2b19f97813a3994d5e6ccd01e9a21ae73b755f7114ac4247fdf5"},
+]
 
 [package.dependencies]
 Deprecated = "*"
@@ -873,6 +1526,10 @@ description = "sphinxcontrib-applehelp is a Sphinx extension which outputs Apple
 category = "dev"
 optional = false
 python-versions = ">=3.8"
+files = [
+    {file = "sphinxcontrib-applehelp-1.0.4.tar.gz", hash = "sha256:828f867945bbe39817c210a1abfd1bc4895c8b73fcaade56d45357a348a07d7e"},
+    {file = "sphinxcontrib_applehelp-1.0.4-py3-none-any.whl", hash = "sha256:29d341f67fb0f6f586b23ad80e072c8e6ad0b48417db2bde114a4c9746feb228"},
+]
 
 [package.extras]
 lint = ["docutils-stubs", "flake8", "mypy"]
@@ -885,6 +1542,9 @@ description = "Sphinx \"contentui\" extension"
 category = "dev"
 optional = false
 python-versions = "*"
+files = [
+    {file = "sphinxcontrib_contentui-0.2.5-py3-none-any.whl", hash = "sha256:a01c7a0cfe360c99692999d3286b6a4d93ebfc94d0eff2619622fd5e6086ab36"},
+]
 
 [package.dependencies]
 Sphinx = ">=2.0"
@@ -896,6 +1556,10 @@ description = "sphinxcontrib-devhelp is a sphinx extension which outputs Devhelp
 category = "dev"
 optional = false
 python-versions = ">=3.5"
+files = [
+    {file = "sphinxcontrib-devhelp-1.0.2.tar.gz", hash = "sha256:ff7f1afa7b9642e7060379360a67e9c41e8f3121f2ce9164266f61b9f4b338e4"},
+    {file = "sphinxcontrib_devhelp-1.0.2-py2.py3-none-any.whl", hash = "sha256:8165223f9a335cc1af7ffe1ed31d2871f325254c0423bc0c4c7cd1c1e4734a2e"},
+]
 
 [package.extras]
 lint = ["docutils-stubs", "flake8", "mypy"]
@@ -908,6 +1572,10 @@ description = "sphinxcontrib-htmlhelp is a sphinx extension which renders HTML h
 category = "dev"
 optional = false
 python-versions = ">=3.8"
+files = [
+    {file = "sphinxcontrib-htmlhelp-2.0.1.tar.gz", hash = "sha256:0cbdd302815330058422b98a113195c9249825d681e18f11e8b1f78a2f11efff"},
+    {file = "sphinxcontrib_htmlhelp-2.0.1-py3-none-any.whl", hash = "sha256:c38cb46dccf316c79de6e5515e1770414b797162b23cd3d06e67020e1d2a6903"},
+]
 
 [package.extras]
 lint = ["docutils-stubs", "flake8", "mypy"]
@@ -920,6 +1588,10 @@ description = "Sphinx extension for thumbnails"
 category = "dev"
 optional = false
 python-versions = "*"
+files = [
+    {file = "sphinxcontrib-images-0.9.4.tar.gz", hash = "sha256:f6c237d0430793e65d91dbddb13b1fb26a2cf838040a9deeb52112969fbc4a4b"},
+    {file = "sphinxcontrib_images-0.9.4-py2.py3-none-any.whl", hash = "sha256:8863e8e8533a116f45cb92523938ab25879cc31dc594f5de4c3dbd9ab3d440b0"},
+]
 
 [package.dependencies]
 requests = ">2.2,<3"
@@ -932,6 +1604,10 @@ description = "A sphinx extension which renders display math in HTML via JavaScr
 category = "dev"
 optional = false
 python-versions = ">=3.5"
+files = [
+    {file = "sphinxcontrib-jsmath-1.0.1.tar.gz", hash = "sha256:a9925e4a4587247ed2191a22df5f6970656cb8ca2bd6284309578f2153e0c4b8"},
+    {file = "sphinxcontrib_jsmath-1.0.1-py2.py3-none-any.whl", hash = "sha256:2ec2eaebfb78f3f2078e73666b1415417a116cc848b72e5172e596c871103178"},
+]
 
 [package.extras]
 test = ["flake8", "mypy", "pytest"]
@@ -943,6 +1619,10 @@ description = "sphinxcontrib-qthelp is a sphinx extension which outputs QtHelp d
 category = "dev"
 optional = false
 python-versions = ">=3.5"
+files = [
+    {file = "sphinxcontrib-qthelp-1.0.3.tar.gz", hash = "sha256:4c33767ee058b70dba89a6fc5c1892c0d57a54be67ddd3e7875a18d14cba5a72"},
+    {file = "sphinxcontrib_qthelp-1.0.3-py2.py3-none-any.whl", hash = "sha256:bd9fc24bcb748a8d51fd4ecaade681350aa63009a347a8c14e637895444dfab6"},
+]
 
 [package.extras]
 lint = ["docutils-stubs", "flake8", "mypy"]
@@ -955,6 +1635,10 @@ description = "sphinxcontrib-serializinghtml is a sphinx extension which outputs
 category = "dev"
 optional = false
 python-versions = ">=3.5"
+files = [
+    {file = "sphinxcontrib-serializinghtml-1.1.5.tar.gz", hash = "sha256:aa5f6de5dfdf809ef505c4895e51ef5c9eac17d0f287933eb49ec495280b6952"},
+    {file = "sphinxcontrib_serializinghtml-1.1.5-py2.py3-none-any.whl", hash = "sha256:352a9a00ae864471d3a7ead8d7d79f5fc0b57e8b3f95e9867eb9eb28999b92fd"},
+]
 
 [package.extras]
 lint = ["docutils-stubs", "flake8", "mypy"]
@@ -967,6 +1651,9 @@ description = "An extension to use emoji codes in your Sphinx documentation"
 category = "dev"
 optional = false
 python-versions = "*"
+files = [
+    {file = "sphinxemoji-0.2.0.tar.gz", hash = "sha256:27861d1dd7c6570f5e63020dac9a687263f7481f6d5d6409eb31ecebcc804e4c"},
+]
 
 [package.dependencies]
 sphinx = ">=1.8"
@@ -978,6 +1665,10 @@ description = "Sphinx Extension to enable OGP support"
 category = "dev"
 optional = false
 python-versions = ">=3.6"
+files = [
+    {file = "sphinxext-opengraph-0.6.3.tar.gz", hash = "sha256:cd89e13cc7a44739f81b64ee57c1c20ef0c05dda5d1d8201d31ec2f34e4c29db"},
+    {file = "sphinxext_opengraph-0.6.3-py3-none-any.whl", hash = "sha256:bf76017c105856b07edea6caf4942b6ae9bb168585dccfd6dbdb6e4161f6b03a"},
+]
 
 [package.dependencies]
 sphinx = ">=2.0"
@@ -989,6 +1680,10 @@ description = "tasks runner for python projects"
 category = "dev"
 optional = false
 python-versions = ">=3.6,<4.0"
+files = [
+    {file = "taskipy-1.10.3-py3-none-any.whl", hash = "sha256:4c0070ca53868d97989f7ab5c6f237525d52ee184f9b967576e8fe427ed9d0b8"},
+    {file = "taskipy-1.10.3.tar.gz", hash = "sha256:112beaf21e3d5569950b99162a1de003fa885fabee9e450757a6b874be914877"},
+]
 
 [package.dependencies]
 colorama = ">=0.4.4,<0.5.0"
@@ -1003,6 +1698,10 @@ description = "Python Library for Tom's Obvious, Minimal Language"
 category = "main"
 optional = false
 python-versions = ">=2.6, !=3.0.*, !=3.1.*, !=3.2.*"
+files = [
+    {file = "toml-0.10.2-py2.py3-none-any.whl", hash = "sha256:806143ae5bfb6a3c6e736a764057db0e6a0e05e338b5630894a5f779cabb4f9b"},
+    {file = "toml-0.10.2.tar.gz", hash = "sha256:b3bda1d108d5dd99f4a20d24d9c348e91c4db7ab1b749200bded2f839ccbe68f"},
+]
 
 [[package]]
 name = "tomli"
@@ -1011,6 +1710,10 @@ description = "A lil' TOML parser"
 category = "dev"
 optional = false
 python-versions = ">=3.7"
+files = [
+    {file = "tomli-2.0.1-py3-none-any.whl", hash = "sha256:939de3e7a6161af0c887ef91b7d41a53e7c5a1ca976325f429cb46ea9bc30ecc"},
+    {file = "tomli-2.0.1.tar.gz", hash = "sha256:de526c12914f0c550d15924c62d72abc48d6fe7364aa87328337a31007fe8a4f"},
+]
 
 [[package]]
 name = "tornado"
@@ -1019,6 +1722,19 @@ description = "Tornado is a Python web framework and asynchronous networking lib
 category = "dev"
 optional = false
 python-versions = ">= 3.7"
+files = [
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+    {file = "tornado-6.2-cp37-abi3-musllinux_1_1_x86_64.whl", hash = "sha256:1d54d13ab8414ed44de07efecb97d4ef7c39f7438cf5e976ccd356bebb1b5fca"},
+    {file = "tornado-6.2-cp37-abi3-win32.whl", hash = "sha256:5c87076709343557ef8032934ce5f637dbb552efa7b21d08e89ae7619ed0eb23"},
+    {file = "tornado-6.2-cp37-abi3-win_amd64.whl", hash = "sha256:e5f923aa6a47e133d1cf87d60700889d7eae68988704e20c75fb2d65677a8e4b"},
+    {file = "tornado-6.2.tar.gz", hash = "sha256:9b630419bde84ec666bfd7ea0a4cb2a8a651c2d5cccdbdd1972a0c859dfc3c13"},
+]
 
 [[package]]
 name = "typing-extensions"
@@ -1027,6 +1743,10 @@ description = "Backported and Experimental Type Hints for Python 3.7+"
 category = "dev"
 optional = false
 python-versions = ">=3.7"
+files = [
+    {file = "typing_extensions-4.5.0-py3-none-any.whl", hash = "sha256:fb33085c39dd998ac16d1431ebc293a8b3eedd00fd4a32de0ff79002c19511b4"},
+    {file = "typing_extensions-4.5.0.tar.gz", hash = "sha256:5cb5f4a79139d699607b3ef622a1dedafa84e115ab0024e0d9c044a9479ca7cb"},
+]
 
 [[package]]
 name = "unidecode"
@@ -1035,6 +1755,10 @@ description = "ASCII transliterations of Unicode text"
 category = "dev"
 optional = false
 python-versions = ">=3.5"
+files = [
+    {file = "Unidecode-1.3.6-py3-none-any.whl", hash = "sha256:547d7c479e4f377b430dd91ac1275d593308dce0fc464fb2ab7d41f82ec653be"},
+    {file = "Unidecode-1.3.6.tar.gz", hash = "sha256:fed09cf0be8cf415b391642c2a5addfc72194407caee4f98719e40ec2a72b830"},
+]
 
 [[package]]
 name = "urllib3"
@@ -1043,6 +1767,10 @@ description = "HTTP library with thread-safe connection pooling, file post, and
 category = "main"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*"
+files = [
+    {file = "urllib3-1.26.15-py2.py3-none-any.whl", hash = "sha256:aa751d169e23c7479ce47a0cb0da579e3ede798f994f5816a74e4f4500dcea42"},
+    {file = "urllib3-1.26.15.tar.gz", hash = "sha256:8a388717b9476f934a21484e8c8e61875ab60644d29b9b39e11e4b9dc1c6b305"},
+]
 
 [package.extras]
 brotli = ["brotli (>=1.0.9)", "brotlicffi (>=0.8.0)", "brotlipy (>=0.6.0)"]
@@ -1056,719 +1784,7 @@ description = "Module for decorators, wrappers and monkey patching."
 category = "dev"
 optional = false
 python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,>=2.7"
-
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-    {file = "urllib3-1.26.15-py2.py3-none-any.whl", hash = "sha256:aa751d169e23c7479ce47a0cb0da579e3ede798f994f5816a74e4f4500dcea42"},
-    {file = "urllib3-1.26.15.tar.gz", hash = "sha256:8a388717b9476f934a21484e8c8e61875ab60644d29b9b39e11e4b9dc1c6b305"},
-]
-wrapt = [
+files = [
     {file = "wrapt-1.15.0-cp27-cp27m-macosx_10_9_x86_64.whl", hash = "sha256:ca1cccf838cd28d5a0883b342474c630ac48cac5df0ee6eacc9c7290f76b11c1"},
     {file = "wrapt-1.15.0-cp27-cp27m-manylinux1_i686.whl", hash = "sha256:e826aadda3cae59295b95343db8f3d965fb31059da7de01ee8d1c40a60398b29"},
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@@ -1845,3 +1861,8 @@ wrapt = [
     {file = "wrapt-1.15.0-py3-none-any.whl", hash = "sha256:64b1df0f83706b4ef4cfb4fb0e4c2669100fd7ecacfb59e091fad300d4e04640"},
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 ]
+
+[metadata]
+lock-version = "2.0"
+python-versions = "^3.10"
+content-hash = "f144fd682ba4c3131bc89e61b6c890049ba35a8f56ab45770d9c344899faf3d0"

From 1c6a9425df34573f9174f565804c4b8d140fb284 Mon Sep 17 00:00:00 2001
From: Oliver Bertuch <o.bertuch@fz-juelich.de>
Date: Wed, 17 May 2023 15:27:53 +0200
Subject: [PATCH 08/21] docs: remove the CLI page from the toctree for now
 until this is more polished

---
 docs/source/index.md | 10 ++++++----
 1 file changed, 6 insertions(+), 4 deletions(-)

diff --git a/docs/source/index.md b/docs/source/index.md
index 0d6e6e17..bb06bb5a 100644
--- a/docs/source/index.md
+++ b/docs/source/index.md
@@ -35,6 +35,12 @@ automatic submission to publication repositories.
 
 ## Documentation
  
+<!--
+```{toctree}
+ cli
+```
+-->
+
 ```{toctree}
 :glob:
 :maxdepth: 1
@@ -42,10 +48,6 @@ automatic submission to publication repositories.
 tutorials/*
 ```
 
-```{toctree}
-cli
-```
-
 ```{toctree}
 :maxdepth: 1
 :caption: Developers

From af1c92bbf081559f4b7b10f9d178a918080c411f Mon Sep 17 00:00:00 2001
From: "Druskat, Stephan" <stephan.druskat@dlr.de>
Date: Wed, 17 May 2023 15:37:04 +0200
Subject: [PATCH 09/21] Remove CLI Usage section

---
 docs/source/cli.rst | 16 ----------------
 1 file changed, 16 deletions(-)
 delete mode 100644 docs/source/cli.rst

diff --git a/docs/source/cli.rst b/docs/source/cli.rst
deleted file mode 100644
index fd032c8a..00000000
--- a/docs/source/cli.rst
+++ /dev/null
@@ -1,16 +0,0 @@
-..
-    SPDX-FileCopyrightText: 2023 Forschungszentrum Jülich
-    SPDX-License-Identifier: CC-BY-SA-4.0
-    SPDX-FileContributor: Oliver Bertuch
-
-..
-    This page must use reStructuredText rather than Markdown to enable parsing and formating the rst-based
-    output of the sphinx-click plugin.
-
-CLI Usage
-=========
-
-.. click:: hermes.cli:main
-  :prog: hermes
-  :nested: full
-

From 8e9abe87adede801407cff1feb15f0e10fce382d Mon Sep 17 00:00:00 2001
From: "Druskat, Stephan" <stephan.druskat@dlr.de>
Date: Wed, 17 May 2023 16:26:30 +0200
Subject: [PATCH 10/21] Update tutorial to use CI template

---
 .../tutorials/001-prepare-your-project.md     | 291 ------------------
 .../automated-publication-with-ci.md          | 143 +++++++++
 2 files changed, 143 insertions(+), 291 deletions(-)
 delete mode 100644 docs/source/tutorials/001-prepare-your-project.md
 create mode 100644 docs/source/tutorials/automated-publication-with-ci.md

diff --git a/docs/source/tutorials/001-prepare-your-project.md b/docs/source/tutorials/001-prepare-your-project.md
deleted file mode 100644
index dcdce966..00000000
--- a/docs/source/tutorials/001-prepare-your-project.md
+++ /dev/null
@@ -1,291 +0,0 @@
-<!--
-SPDX-FileCopyrightText: 2023 German Aerospace Center (DLR), Forschungszentrum Jülich GmbH
-
-SPDX-License-Identifier: CC-BY-SA-4.0
--->
-
-<!-- 
-SPDX-FileContributor: Oliver Bertuch
-SPDX-FileContributor: Michael Meinel
--->
-
-# T01: Add HERMES to your project
- 
-In this tutorial we will guide you through the process of preparing your project for metadata publication.
-
-```{note}
-We assume that you have a project that is stored in a Git code repository on GitHub.
-```
- 
-We use the [HERMES showcase repo](https://github.com/hermes-hmc/showcase) throughout this tutorial.
-It should be easily adoptable to other code repositories.
- 
-## Clone the example code repository
- 
-This step is optional if you use a checked-out version of your own code repository.
- 
-```shell
-git clone https://github.com/hermes-hmc/showcase.git hermes-showcase
-cd hermes-showcase
-```
- 
-Your directory should look like the following:
- 
-```{code-block}
----
-linenos: True
----
-.
-├── CITATION.cff
-├── .github
-│   └── workflows
-│       └── hermes.yml
-├── .gitignore
-├── hermes.toml
-├── LICENSE
-├── pyproject.toml
-├── README.md
-└── src
-    └── showcase
-        ├── hello.py
-        └── __init__.py
-```
-
-(Again: if you use this for your own project, your mileage will vary.)
-
-At this point, the important files for HERMES are `CITATION.cff` (structured metadata), `hermes.toml`
-(workflow configuration) and `.github/workflows/hermes.yml` (CI job for publication).
- 
-## Test-drive hermes
- 
-You can run the workflow locally to verify results before adding it to your continuous integration configuration.
-
-Installation assumes you have `python` v3.10+ installed:
-
-```shell
-pip install "git+https://github.com/hermes-hmc/workflow.git@deRSE23"
-```
-
-Once installed, simply run the workflow:
-
-```shell
-hermes
-```
-
-The output will look like follows, indicating metadata is collated from `CITATION.cff` and `Git` history:
-
-```text
-hermes workflow (0.1.0)
-=======================
-
-Workflow to publish research software with rich metadata
-
-# Running Hermes
-Running Hermes command line in: <some place you checked out the showcase>/hermes-showcase
-# Metadata harvesting
-- Running harvester cff
-
-## Citation File Format
-
-- Running harvester git
-
-## Git History
-
-
-# Metadata processing
-## Process data from cff
-
-### Add author names
-
-## Process data from git
-
-### Add git authors and committers as contributors
-
-### Add git branch
-```
-
-You can see that there are only two stages of the pipeline executed, "harvesting" and "processing".
-This is the default behavior as you certainly want to review the results, especially if you just started
-adding metadata to your code repository.
- 
-If you look at your working directory, it should look similar to this:
-
-```{code-block}
----
-linenos: True
----
-.
-├── .github
-│   └── workflows
-│       └── hermes.yml
-├── .gitignore
-├── .hermes
-│   ├── harvest
-│   │   ├── cff.json
-│   │   └── git.json
-│   └── process
-│       ├── codemeta.json
-│       └── tags.json
-├── hermes-audit.md
-├── hermes.log
-├── hermes.toml
-├── LICENSE
-├── pyproject.toml
-├── README.md
-└── src
-    └── showcase
-        ├── hello.py
-        └── __init__.py
-```
-
-Note the new directory `.hermes`. This is automatically created and maintained by the workflow to store the metadata
-at the different stages. Inside that folder you will find a sub-folder for every stage.
-The cache files are JSON and can be inspected to investigate into the results of the different stages.
-
-Also new are the files `hermes-audit.md` and `hermes.log`. You may ignore both for now, they currently are mostly
-useful for development and debugging.
-
-
-## Configure your .gitignore
- 
-As the `.hermes` folder contains transient caches, it is a good idea to not store it in your code repository.
-Hence, it is a good idea to add this folder to your `.gitignore` file, along with the log files.
- 
-Create a new `.gitignore` and add `.hermes` to it:
- 
-```
-echo ".hermes" >> .gitignore
-echo "hermes.log" >> .gitignore
-echo "hermes-audit.md" >> .gitignore
-```
-
-(This has already been done in the `showcase` project)
- 
-## Provide additional metadata using CITATION.cff
- 
-Until now, there is not much metadata to publish for your project.
-We will change this by adding a [`CITATION.cff`](https://citation-file-format.github.io/) file to your code repository.
-This file stores metadata about the authors of a software project and how to reference it in publications.
-
-The `showcase` project contains a fake but working example as outlined above.
-You may copy [this example file](https://github.com/hermes-hmc/showcase/blob/main/CITATION.cff) to your own project 
-and adapt or use [cffinit](https://citation-file-format.github.io/cff-initializer-javascript/) to start anew.
- 
-Please make sure to add your own `CITATION.cff` to your version controlled project.
- 
-## Configuration of your project
- 
-The HERMES workflow is fully configurable via a [TOML](https://toml.io) file `hermes.toml`.
-This file is structured by having a table for each step of the workflow:
-
-```toml
-[harvest]
-[process]
-[deposit]
-[postprocess]
-```
-
-HERMES has opinionated defaults, living the "convention over configuration" paradigm, for every step.
-If you are not satisfied with the defaults, you can override anything by applying your own configuration.
-
-The `showcase` repository contains a `hermes.toml`, which as an example
-
-- configures to include the Git and Citation File Format metadata harvesters only,
-- disables validation in the CFF file harvester,
-- activates mapping and deposition to an Invenio based repository,
-- and configures the Zenodo Sandbox as the target publication repository:
-
-```toml
-[harvest]
-from = [ "cff", "git" ]
-
-[harvest.cff]
-validate = false
-
-[deposit]
-mapping = "invenio"
-target = "invenio"
-
-[deposit.invenio]
-base_url = "https://sandbox.zenodo.org"
-```
-
-Simply copy and paste this file to your own project for now just to get started.
-
-```{note}
-Right now, the HERMES workflow only supports a limited number of operations in its "Proof Of Concept" state.
-Expect a bumpy ride when trying to alter this minimal configuration.
-```
-
-## Optional: Testing depositing locally
-
-Targeting the Zenodo Sandbox, please [receive a "Personal Access Token" from them via your user profile](https://sandbox.zenodo.org/account/settings/applications/tokens/new/)
-with the scopes `deposit:actions` and `deposit:write` so the workflow can act on your behalf.
-
-Before executing a deposition, please think about whether you want to include your software as an artifact in it.
-A simple example to do that is to create a ZIP file of your sources, here using the `showcase` project:
-
-```shell
-git archive --format zip HEAD src > showcase.zip
-```
-
-To create a software publication that also includes the software artifact now run:
-
-```shell
-hermes deposit --auth-token <PAT here> --file README.md --file showcase.zip
-```
-
-If all goes well, you will find the URL of the deposit in the output:
-```text
-hermes workflow (0.1.0)
-=======================
-
-Workflow to publish research software with rich metadata
-
-# Running Hermes
-Running Hermes command line in: <some place you checked out the showcase>/hermes-showcase
-Metadata deposition
-Published record: https://sandbox.zenodo.org/record/1166086
-```
-
-## Add a deposit job via CI
-
-```{note}
-This example uses Github Action syntax, but can be transfered to Jenkins or GitLab CI syntax.
-```
-
-Add a file `.github/workflows/hermes.yaml` to your project by copy and pasting
-[the example from the `showcase` project](https://github.com/hermes-hmc/showcase/blob/main/.github/workflows/hermes.yml):
-
-```yaml
-name: Software Publication
-
-on:
-  tags: # Change as you see fit for your project!
-
-jobs:
-  hermes:
-    name: HERMES
-    runs-on: ubuntu-latest
-    permissions:
-      contents: read # We will only read content from the repo
-      # pull-requests: write # Postprocessing should be able to create a pull request with changes
-    steps:
-      - uses: actions/checkout@v2
-      - uses: actions/setup-python@v4
-        with:
-          python-version: '3.10'
-      - run: pip install git+https://github.com/hermes-hmc/workflow.git@deRSE23
-      - run: git archive --format zip HEAD src > showcase.zip
-      - run: hermes
-      - run: hermes deposit --auth-token ${{ secrets.ZENODO_SANDBOX }} --file showcase.zip --file README.md
-      # - run: hermes postprocess # (Not implemented yet)
-      # - uses: peter-evans/create-pull-request@v4 (TODO once postprocessing has it)
-```
-
-Within this workflow, we use a secret called `ZENODO_SANBOX`, which you will need to
-[add to your Github repository](https://docs.github.com/en/actions/security-guides/encrypted-secrets#creating-encrypted-secrets-for-a-repository)
-and contains your "Personal Access Token".
-
-Now, once you create a new Git tag in your code repository, the HERMES workflow will create a rich metadata
-software publication for you within the Zenodo Sandbox.
diff --git a/docs/source/tutorials/automated-publication-with-ci.md b/docs/source/tutorials/automated-publication-with-ci.md
new file mode 100644
index 00000000..5e3a392e
--- /dev/null
+++ b/docs/source/tutorials/automated-publication-with-ci.md
@@ -0,0 +1,143 @@
+<!--
+SPDX-FileCopyrightText: 2023 German Aerospace Center (DLR), Forschungszentrum Jülich GmbH
+
+SPDX-License-Identifier: CC-BY-SA-4.0
+-->
+
+<!-- 
+SPDX-FileContributor: Oliver Bertuch
+SPDX-FileContributor: Michael Meinel
+SPDX-FileContributor: Stephan Druskat
+-->
+
+# Set up automatic software publishing
+ 
+```{note}
+This tutorial works for repositories hosted on GitHub, and shows how to automatically publish to Zenodo Sandbox.
+Zenodo Sandbox is a "toy" repository that can be used to try things out.
+
+This tutorial should also work with the "real" Zenodo.
+```
+ 
+## Configure your .gitignore
+ 
+The HERMES workflow (`hermes`) uses temporary caches in `.hermes/`.
+Ignore this directory in your git repository: 
+
+Add `.hermes/` to your `.gitignore` file:
+ 
+```bash
+# .gitignore
+
+.hermes/
+```
+
+## Provide additional metadata using CITATION.cff
+ 
+To provide high-quality citation metadata for your project and your publication,
+provide a `CITATION.cff` file in the [Citation File Format](https://citation-file-format.github.io/).
+
+If you don't have one yet,
+use the [cffinit](https://citation-file-format.github.io/cff-initializer-javascript/) website
+to create a `CITATION.cff` file.
+Save it to the root directory of your repository, and add it to version control.
+
+```bash
+git add CITATION.cff
+git commit -m "Add citation file"
+git push
+```
+ 
+## HERMES configuration
+ 
+The HERMES workflow is configured in a [TOML](https://toml.io) file: `hermes.toml`.
+Each step in the publication workflow has its own section.
+
+Configure HERMES to:
+
+- harvest metadata from Git and `CITATION.cff`
+- skip validation of `CITATION.cff`
+- deposit on Zenodo Sandbox (which is built on the InvenioRDM)
+- use Zenodo Sandbox as the target publication repository
+
+```toml
+[harvest]
+from = [ "cff", "git" ]
+
+[harvest.cff]
+validate = false
+
+[deposit]
+mapping = "invenio"
+target = "invenio"
+
+[deposit.invenio]
+base_url = "https://sandbox.zenodo.org"
+```
+
+Copy this file to your repository and add it to version control:
+
+```bash
+git add hermes.toml
+git commit -m "Configure HERMES to harvest git and CFF, and deposit on Zenodo Sandbox"
+git push
+```
+
+## Get a personal access token for Zenodo Sandbox
+
+To allow GitHub Actions to publish our repository to Zenodo Sandbox for us,
+we need a personal access token from Zenodo Sandbox.
+
+Log in at https://sandbox.zenodo.org (you may have to register first),
+then [create a personal access token in your user profile](https://sandbox.zenodo.org/account/settings/applications/tokens/new/)
+with the scopes `deposit:actions` and `deposit:write`.
+
+Copy the newly created token into a new [GitHub Secret](https://docs.github.com/en/actions/security-guides/encrypted-secrets#creating-encrypted-secrets-for-a-repository) called `ZENODO_SANDBOX` in your repository.
+
+## Configure a GitHub Action to automate publication 
+
+The HERMES project provides templates for continous integration systems in a dedicated repository:
+https://github.com/hermes-hmc/ci-templates.
+
+Copy the [template for GitHub to Zenodo Sandbox publication](https://github.com/hermes-hmc/ci-templates/blob/main/TEMPLATE_hermes_github_to_zenodo.yml)
+into the `.github/workflows/` directory in your repository, and rename it as you like (e.g. `hermes_github_to_zenodo.yml`).
+
+Go through the file, and look for comments marked with `# ADAPT`.
+Adapt the file to your needs.
+If you need help with how GitHub Action workflows work in general,
+have a look at the [documentation on GitHub](https://docs.github.com/actions).
+
+Add the workflow file to version control and push it.
+
+```{warning}
+If you haven't adapted the workflow file, and push it to the branch `main`, you will create an automatic publication at this point.
+```
+
+```bash
+git add .github/workflows/hermes_github_to_zenodo.yml
+git commit -m "Configure automatic publication with HERMES"
+git push
+```
+
+## Automatic publication workflow
+
+```{success}
+Congratulations, you can now automatically publish your repository to Zenodo Sandbox!
+```
+
+Now, whenever the GitHub Actions workflow is triggered, it will publish a new version of your repository to Zenodo Sandbox.
+If you haven't adapted the workflow file, this will happen whenever you push to your `main` branch.
+
+<!-- TODO: Add user workflow chart here? -->
+
+When the workflow runs, it harvests and processes the metadata from Git and your `CITATION.cff` file,
+and creates a new pull request in your repository.
+You then have the chance to curate the metadata, i.e., make sure that it looks the way you want.
+If you merge the pull request, the actual publication is created, 
+and the HERMES configuration file is updated 
+with the ID of the publication.
+This is needed so that future published versions are collected under the same *concept DOI*.
+
+If the updates from the publication actually change the configuration file, or the `CITATION.cff` file,
+HERMES will create another pull request after publication.
+In this pull request, you can accept or reject the changes that are made.

From 240c06859fc47f2060914ad28be26c6e094c9320 Mon Sep 17 00:00:00 2001
From: "Druskat, Stephan" <stephan.druskat@dlr.de>
Date: Wed, 17 May 2023 16:33:33 +0200
Subject: [PATCH 11/21] Update callout role

---
 docs/source/tutorials/automated-publication-with-ci.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/source/tutorials/automated-publication-with-ci.md b/docs/source/tutorials/automated-publication-with-ci.md
index 5e3a392e..fc8d60c4 100644
--- a/docs/source/tutorials/automated-publication-with-ci.md
+++ b/docs/source/tutorials/automated-publication-with-ci.md
@@ -121,7 +121,7 @@ git push
 
 ## Automatic publication workflow
 
-```{success}
+```{note}
 Congratulations, you can now automatically publish your repository to Zenodo Sandbox!
 ```
 

From a5c2b08cfe0be465ec0fbfc7ff793a1e672c7d80 Mon Sep 17 00:00:00 2001
From: "Druskat, Stephan" <stephan.druskat@dlr.de>
Date: Wed, 17 May 2023 18:21:09 +0200
Subject: [PATCH 12/21] Add link to Zenodo versioning docs

---
 docs/source/tutorials/automated-publication-with-ci.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/source/tutorials/automated-publication-with-ci.md b/docs/source/tutorials/automated-publication-with-ci.md
index fc8d60c4..6897f125 100644
--- a/docs/source/tutorials/automated-publication-with-ci.md
+++ b/docs/source/tutorials/automated-publication-with-ci.md
@@ -136,7 +136,7 @@ You then have the chance to curate the metadata, i.e., make sure that it looks t
 If you merge the pull request, the actual publication is created, 
 and the HERMES configuration file is updated 
 with the ID of the publication.
-This is needed so that future published versions are collected under the same *concept DOI*.
+This is needed so that future published versions are collected under the same [*concept DOI*](https://help.zenodo.org/#versioning).
 
 If the updates from the publication actually change the configuration file, or the `CITATION.cff` file,
 HERMES will create another pull request after publication.

From 4dbabe3f94024d6f02d03e521e55eadc54d16980 Mon Sep 17 00:00:00 2001
From: Stephan Druskat <sdruskat@users.noreply.github.com>
Date: Mon, 22 May 2023 10:41:38 +0200
Subject: [PATCH 13/21] Update
 docs/source/tutorials/automated-publication-with-ci.md

---
 docs/source/tutorials/automated-publication-with-ci.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/source/tutorials/automated-publication-with-ci.md b/docs/source/tutorials/automated-publication-with-ci.md
index 6897f125..0495460c 100644
--- a/docs/source/tutorials/automated-publication-with-ci.md
+++ b/docs/source/tutorials/automated-publication-with-ci.md
@@ -22,7 +22,7 @@ This tutorial should also work with the "real" Zenodo.
 ## Configure your .gitignore
  
 The HERMES workflow (`hermes`) uses temporary caches in `.hermes/`.
-Ignore this directory in your git repository: 
+Ignore this directory in your git repository.
 
 Add `.hermes/` to your `.gitignore` file:
  

From bfab22989ba85c233d7e28d6d366f76c4dc78540 Mon Sep 17 00:00:00 2001
From: Oliver Bertuch <o.bertuch@fz-juelich.de>
Date: Mon, 22 May 2023 17:30:43 +0200
Subject: [PATCH 14/21] docs: add Mermaid support for nice diagrams from within
 Sphinx

---
 docs/source/conf.py |  1 +
 poetry.lock         | 14 +++++++++++++-
 pyproject.toml      |  1 +
 3 files changed, 15 insertions(+), 1 deletion(-)

diff --git a/docs/source/conf.py b/docs/source/conf.py
index c7464f9c..c7467919 100644
--- a/docs/source/conf.py
+++ b/docs/source/conf.py
@@ -56,6 +56,7 @@
     'myst_parser',
     'autoapi.extension',
     'sphinx_click',
+    'sphinxcontrib.mermaid',
 ]
 
 language = 'en'
diff --git a/poetry.lock b/poetry.lock
index 961858b4..abab7d6c 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1612,6 +1612,18 @@ files = [
 [package.extras]
 test = ["flake8", "mypy", "pytest"]
 
+[[package]]
+name = "sphinxcontrib-mermaid"
+version = "0.8.1"
+description = "Mermaid diagrams in yours Sphinx powered docs"
+category = "dev"
+optional = false
+python-versions = ">=3.7"
+files = [
+    {file = "sphinxcontrib-mermaid-0.8.1.tar.gz", hash = "sha256:fa3e5325d4ba395336e6137d113f55026b1a03ccd115dc54113d1d871a580466"},
+    {file = "sphinxcontrib_mermaid-0.8.1-py3-none-any.whl", hash = "sha256:15491c24ec78cf1626b1e79e797a9ce87cb7959cf38f955eb72dd5512aeb6ce9"},
+]
+
 [[package]]
 name = "sphinxcontrib-qthelp"
 version = "1.0.3"
@@ -1865,4 +1877,4 @@ files = [
 [metadata]
 lock-version = "2.0"
 python-versions = "^3.10"
-content-hash = "f144fd682ba4c3131bc89e61b6c890049ba35a8f56ab45770d9c344899faf3d0"
+content-hash = "eb51c7be4303f758bee5708107040530556ca7d518b2945572a7e09a4155c30f"
diff --git a/pyproject.toml b/pyproject.toml
index 247d8b73..59bf699c 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -67,6 +67,7 @@ sphinx-autoapi = "^2.0.0"
 sphinxemoji = "^0.2.0"
 sphinxext-opengraph = "^0.6.3"
 sphinx-click = "^4.4.0"
+sphinxcontrib-mermaid="^0.8.1"
 reuse = "^1.0.0"
 
 [tool.poetry.plugins.console_scripts]

From 3160783524c2df7dee1af552aaa39a206724d5dd Mon Sep 17 00:00:00 2001
From: Oliver Bertuch <o.bertuch@fz-juelich.de>
Date: Mon, 22 May 2023 17:31:30 +0200
Subject: [PATCH 15/21] docs: some tweaks to the code blocks and admonitions

---
 .../tutorials/automated-publication-with-ci.md      | 13 ++++++++-----
 1 file changed, 8 insertions(+), 5 deletions(-)

diff --git a/docs/source/tutorials/automated-publication-with-ci.md b/docs/source/tutorials/automated-publication-with-ci.md
index 0495460c..e32dbb12 100644
--- a/docs/source/tutorials/automated-publication-with-ci.md
+++ b/docs/source/tutorials/automated-publication-with-ci.md
@@ -26,8 +26,8 @@ Ignore this directory in your git repository.
 
 Add `.hermes/` to your `.gitignore` file:
  
-```bash
-# .gitignore
+```{code-block} bash
+:caption: .gitignore
 
 .hermes/
 ```
@@ -60,7 +60,10 @@ Configure HERMES to:
 - deposit on Zenodo Sandbox (which is built on the InvenioRDM)
 - use Zenodo Sandbox as the target publication repository
 
-```toml
+```{code-block} toml
+:caption: hermes.toml
+:name: hermes.toml
+
 [harvest]
 from = [ "cff", "git" ]
 
@@ -121,8 +124,8 @@ git push
 
 ## Automatic publication workflow
 
-```{note}
-Congratulations, you can now automatically publish your repository to Zenodo Sandbox!
+```{admonition} Congratulations!
+You can now automatically publish your repository to Zenodo Sandbox!
 ```
 
 Now, whenever the GitHub Actions workflow is triggered, it will publish a new version of your repository to Zenodo Sandbox.

From 083e0d1d3df4738aedb735501b6bac937db0e85f Mon Sep 17 00:00:00 2001
From: Oliver Bertuch <o.bertuch@fz-juelich.de>
Date: Mon, 22 May 2023 17:32:09 +0200
Subject: [PATCH 16/21] docs: add diagram of Github deposition workflow in a
 margin

---
 .../tutorials/automated-publication-with-ci.md   | 16 +++++++++++++++-
 1 file changed, 15 insertions(+), 1 deletion(-)

diff --git a/docs/source/tutorials/automated-publication-with-ci.md b/docs/source/tutorials/automated-publication-with-ci.md
index e32dbb12..a160f204 100644
--- a/docs/source/tutorials/automated-publication-with-ci.md
+++ b/docs/source/tutorials/automated-publication-with-ci.md
@@ -128,10 +128,24 @@ git push
 You can now automatically publish your repository to Zenodo Sandbox!
 ```
 
+````{margin}
+```{mermaid}
+---
+---
+flowchart TD
+    t(("Trigger\n (i.e. push)")) -->
+    ci1("Run Harvest, Process,\n Curate steps") -->
+    pr1("Create Curation PR") -->
+    d{"Accept?"}
+    d -->|Merge| ci2("Run Deposit &\n Postprocess step") --> pr2("Create PR from\n Postprocessing") --> e((("End")))
+    d -->|Close| ci3("Cleanup") --> e((("End")))
+```
+````
+
 Now, whenever the GitHub Actions workflow is triggered, it will publish a new version of your repository to Zenodo Sandbox.
 If you haven't adapted the workflow file, this will happen whenever you push to your `main` branch.
 
-<!-- TODO: Add user workflow chart here? -->
+The diagram on the right shows the different steps that will happen each time.
 
 When the workflow runs, it harvests and processes the metadata from Git and your `CITATION.cff` file,
 and creates a new pull request in your repository.

From c7104028b8b622f4b12e60f683784c8c87e7949c Mon Sep 17 00:00:00 2001
From: "Druskat, Stephan" <stephan.druskat@dlr.de>
Date: Tue, 23 May 2023 12:28:54 +0200
Subject: [PATCH 17/21] Refine and embed mermaid graph

---
 .../automated-publication-with-ci.md          | 43 ++++++++++---------
 1 file changed, 23 insertions(+), 20 deletions(-)

diff --git a/docs/source/tutorials/automated-publication-with-ci.md b/docs/source/tutorials/automated-publication-with-ci.md
index a160f204..7ac93714 100644
--- a/docs/source/tutorials/automated-publication-with-ci.md
+++ b/docs/source/tutorials/automated-publication-with-ci.md
@@ -128,33 +128,36 @@ git push
 You can now automatically publish your repository to Zenodo Sandbox!
 ```
 
-````{margin}
-```{mermaid}
----
----
-flowchart TD
-    t(("Trigger\n (i.e. push)")) -->
-    ci1("Run Harvest, Process,\n Curate steps") -->
-    pr1("Create Curation PR") -->
-    d{"Accept?"}
-    d -->|Merge| ci2("Run Deposit &\n Postprocess step") --> pr2("Create PR from\n Postprocessing") --> e((("End")))
-    d -->|Close| ci3("Cleanup") --> e((("End")))
-```
-````
-
 Now, whenever the GitHub Actions workflow is triggered, it will publish a new version of your repository to Zenodo Sandbox.
 If you haven't adapted the workflow file, this will happen whenever you push to your `main` branch.
 
-The diagram on the right shows the different steps that will happen each time.
+The following diagram shows the different steps that will happen each time.
+
+```{mermaid}
+flowchart LR
+    t(("Trigger\nGitHub Action\n(e.g. push)"))
+    rh("Run hermes")
+    subgraph "hermes (harvest, process, curate)"
+    ci1("Harvest & process metadata")
+    pr1("Create curation pull request")
+    end
+    d{"Merge?"}
+    subgraph "hermes (deposit, postprocess)"
+    ci2("Publish software")
+    pp("Postprocessing")
+    pr2("Create pull request\nfrom postprocessing")
+    ci3("Cleanup")
+    end
+    e((("End")))
+    t --> rh --> ci1 --> pr1 --> d -->|Merge| ci2 --> pp --> pr2 --> e
+    d -->|Close| ci3 --> e
+```
 
 When the workflow runs, it harvests and processes the metadata from Git and your `CITATION.cff` file,
 and creates a new pull request in your repository.
 You then have the chance to curate the metadata, i.e., make sure that it looks the way you want.
 If you merge the pull request, the actual publication is created, 
-and the HERMES configuration file is updated 
+and a new pull request is opened to update the HERMES configuration file
+in your repository
 with the ID of the publication.
 This is needed so that future published versions are collected under the same [*concept DOI*](https://help.zenodo.org/#versioning).
-
-If the updates from the publication actually change the configuration file, or the `CITATION.cff` file,
-HERMES will create another pull request after publication.
-In this pull request, you can accept or reject the changes that are made.

From 0b056d4ee6244c94f764f8a98b37307ae4f9dec2 Mon Sep 17 00:00:00 2001
From: "Druskat, Stephan" <stephan.druskat@dlr.de>
Date: Tue, 23 May 2023 12:31:09 +0200
Subject: [PATCH 18/21] Add postprocessing config

---
 docs/source/tutorials/automated-publication-with-ci.md | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/docs/source/tutorials/automated-publication-with-ci.md b/docs/source/tutorials/automated-publication-with-ci.md
index 7ac93714..ee7149ef 100644
--- a/docs/source/tutorials/automated-publication-with-ci.md
+++ b/docs/source/tutorials/automated-publication-with-ci.md
@@ -76,6 +76,9 @@ target = "invenio"
 
 [deposit.invenio]
 base_url = "https://sandbox.zenodo.org"
+
+[postprocess]
+execute = [ "config_record_id" ]
 ```
 
 Copy this file to your repository and add it to version control:

From d86f109f0ac48e4248db3c10a8fc7e0d9cd3702c Mon Sep 17 00:00:00 2001
From: "Druskat, Stephan" <stephan.druskat@dlr.de>
Date: Tue, 23 May 2023 12:36:38 +0200
Subject: [PATCH 19/21] Put graph back in margin

---
 docs/source/tutorials/automated-publication-with-ci.md | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/docs/source/tutorials/automated-publication-with-ci.md b/docs/source/tutorials/automated-publication-with-ci.md
index ee7149ef..e7d699aa 100644
--- a/docs/source/tutorials/automated-publication-with-ci.md
+++ b/docs/source/tutorials/automated-publication-with-ci.md
@@ -134,10 +134,11 @@ You can now automatically publish your repository to Zenodo Sandbox!
 Now, whenever the GitHub Actions workflow is triggered, it will publish a new version of your repository to Zenodo Sandbox.
 If you haven't adapted the workflow file, this will happen whenever you push to your `main` branch.
 
-The following diagram shows the different steps that will happen each time.
+The diagram to the right shows the different steps that will happen each time.
 
+````{margin}
 ```{mermaid}
-flowchart LR
+flowchart TD
     t(("Trigger\nGitHub Action\n(e.g. push)"))
     rh("Run hermes")
     subgraph "hermes (harvest, process, curate)"
@@ -155,6 +156,7 @@ flowchart LR
     t --> rh --> ci1 --> pr1 --> d -->|Merge| ci2 --> pp --> pr2 --> e
     d -->|Close| ci3 --> e
 ```
+````
 
 When the workflow runs, it harvests and processes the metadata from Git and your `CITATION.cff` file,
 and creates a new pull request in your repository.

From e18fadcf74059a30318c4fab4c5e08df0b74ce56 Mon Sep 17 00:00:00 2001
From: "Druskat, Stephan" <stephan.druskat@dlr.de>
Date: Tue, 23 May 2023 12:37:55 +0200
Subject: [PATCH 20/21] Switch order of harvesters in example config

---
 docs/source/tutorials/automated-publication-with-ci.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/source/tutorials/automated-publication-with-ci.md b/docs/source/tutorials/automated-publication-with-ci.md
index e7d699aa..05947a03 100644
--- a/docs/source/tutorials/automated-publication-with-ci.md
+++ b/docs/source/tutorials/automated-publication-with-ci.md
@@ -65,7 +65,7 @@ Configure HERMES to:
 :name: hermes.toml
 
 [harvest]
-from = [ "cff", "git" ]
+from = [ "git", "cff" ]
 
 [harvest.cff]
 validate = false

From e5bd179cffcb8f0606809dd1ba118ca0bac7b011 Mon Sep 17 00:00:00 2001
From: "Druskat, Stephan" <stephan.druskat@dlr.de>
Date: Tue, 23 May 2023 12:43:02 +0200
Subject: [PATCH 21/21] docs: Move diagram up in margin

---
 .../tutorials/automated-publication-with-ci.md | 18 +++++++++---------
 1 file changed, 9 insertions(+), 9 deletions(-)

diff --git a/docs/source/tutorials/automated-publication-with-ci.md b/docs/source/tutorials/automated-publication-with-ci.md
index 05947a03..45d8d063 100644
--- a/docs/source/tutorials/automated-publication-with-ci.md
+++ b/docs/source/tutorials/automated-publication-with-ci.md
@@ -127,15 +127,6 @@ git push
 
 ## Automatic publication workflow
 
-```{admonition} Congratulations!
-You can now automatically publish your repository to Zenodo Sandbox!
-```
-
-Now, whenever the GitHub Actions workflow is triggered, it will publish a new version of your repository to Zenodo Sandbox.
-If you haven't adapted the workflow file, this will happen whenever you push to your `main` branch.
-
-The diagram to the right shows the different steps that will happen each time.
-
 ````{margin}
 ```{mermaid}
 flowchart TD
@@ -158,6 +149,15 @@ flowchart TD
 ```
 ````
 
+```{admonition} Congratulations!
+You can now automatically publish your repository to Zenodo Sandbox!
+```
+
+Now, whenever the GitHub Actions workflow is triggered, it will publish a new version of your repository to Zenodo Sandbox.
+If you haven't adapted the workflow file, this will happen whenever you push to your `main` branch.
+
+The diagram to the right shows the different steps that will happen each time.
+
 When the workflow runs, it harvests and processes the metadata from Git and your `CITATION.cff` file,
 and creates a new pull request in your repository.
 You then have the chance to curate the metadata, i.e., make sure that it looks the way you want.