reorganized repo

01_example_markdown.md

@@ -0,0 +1,20 @@
+---
+title: Example Markdown
+---
+
+You can then embed interactive widget cell outputs inside .ipynb files under `notebooks` using the following notation:
+
+````
+:::{figure} #app:example_widget
+:name: fig_example_widget
+:placeholder: ./figures/example_widget_placeholder.png
+Example widget.
+:::
+````
+
+:::{figure} #app:example_widget
+:name: fig_example_widget
+:placeholder: ./figures/example_widget_placeholder.png
+Example widget.
+:::
+

README.md

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+# Elemental Microscopy Quickstart
+
+This repository contains minimal configuration files to get started for an `Elemental Microscopy` article.
+
+## People
+
+This quickstart guide was developed by [Colin Ophus](mailto:[email protected]) and [Georgios Varnavides](mailto:[email protected]). 
+
+## Installation Instructions
+
+### Edit locally and push changes
+
+> [!WARNING]
+> First, ask one of the organization members to give you `write` access to the forked repo.
+
+> [!WARNING]
+> In what follows and the configuration files, you will see references to `change-to-repo-name`, which you should replace with the repo name. E.g. this article would be `em-quickstart`.
+
+Steps to edit locally:
+- git clone repo (`git clone [email protected]:msa-em/change-to-repo-name.git`)
+- switch to `dev` branch (`git checkout dev`)
+- edit `environment.yml` to
+  - change the environment `name` to the repo name
+  - add your package dependencies, pinning versions as necessary
+- create virtual environment (`conda env create -f environment.yml`)
+  - you might need to remove the environment if it already exists (`conda remove -n change-to-repo-name --all`)
+- activate virtual environment in two terminal windows (`conda activate change-to-repo-name`)
+- edit `myst.yml` file by:
+  - commenting these lines out
+  ```yml
+    jupyter: true
+  ```
+  - uncommenting these lines
+  ```yml
+  #  jupyter:
+    #    server:
+    #      url: 'http://localhost:8888'
+    #      token: '512ac78f14e1141db1fac17e8b4099c1e5bc7d589518b38c'
+  ```
+- start the jupyter server in one of the terminal windows (`jupyter lab --IdentityProvider.token=512ac78f14e1141db1fac17e8b4099c1e5bc7d589518b38c --ServerApp.allow_origin='http://localhost:3000' --port=8888`)
+- start MyST in the other terminal window (`myst start`)
+- edit, commit, and push to `dev` as per usual
+  - make sure **NOT** to commit your `must.yml` changes!
+- open a draft pull request into `main` (if one doesn't already exist) and keep pushing your changes to `dev`
+  - this will enable live previews and checks (see below)
+  - when you're ready, merge pull request into `main`. Note this need to be "final" -- it's best practice to merge thematic content changes together
+
+> [!NOTE]
+> If you don't plan on editing the notebooks, you can skip the `myst.yml` and `jupyter lab` steps above
+
+## Preview draft deployed site
+The repo has two github actions to automatically deploy computational sites, for the following two case:
+- Commits to `main` directly
+- Pull requests into `main`
+
+If you followed the instructions above (i.e. working off of `dev` and have an open pull request into `main`), then you should see a `github-actions` bot at the top of your pull request which will keep getting edited.
+Simply click on the `Inspect` link to see the curvenote staging site, and press `preview` to see the deployed site based on your latest commit.
+

curvenote-export/myst.yml

@@ -0,0 +1,43 @@
+version: 1
+project:
+  title: 'Deep Learning Applications in Microscopy: Segmentation and Tracking'
+  description: ''
+  authors:
+    - userId: PuMpaY9vxJXq7MgyOn06KAJjJFk1
+      nameParsed:
+        literal: Yifei Duan
+        given: Yifei
+        family: Duan
+      name: Yifei Duan
+      corresponding: false
+      roles: []
+      affiliations: []
+      id: contributors-generated-uid-0
+    - userId: eQLn8OuKA6P0tnqqXpwbKjwbFNT2
+      nameParsed:
+        literal: Yifan Duan
+        given: Yifan
+        family: Duan
+      name: Yifan Duan
+      corresponding: false
+      roles: []
+      affiliations: []
+      id: contributors-generated-uid-1
+  affiliations:
+    - id: 24b97dfc-b244-4100-9c61-08dd5654fa58
+      name: 24b97dfc-b244-4100-9c61-08dd5654fa58
+    - id: 7d4aefe9-595b-44a7-8f83-003fe208d7cf
+      name: 7d4aefe9-595b-44a7-8f83-003fe208d7cf
+  id: 23XJ7d092W52UYjknN3G
+  remote: 23XJ7d092W52UYjknN3G
+site:
+  title: 'Deep Learning Applications in Microscopy: Segmentation and Tracking'
+  options:
+    logo_text: 'Deep Learning Applications in Microscopy: Segmentation and Tracking'
+  nav:
+    - title: 'Deep Learning Applications in Microscopy: Segmentation and Tracking'
+      url: /deep-learning-applications-in-microscopy-segmentat
+  actions:
+    - title: Learn More
+      url: https://curvenote.com/docs/web
+  domains: []

environment.yml

@@ -0,0 +1,18 @@
+name: change-this-to-repo-name
+channels:
+  - conda-forge
+dependencies:
+  # add your dependencies below
+  # pinning versions if necessary 
+  - python
+  - numpy
+  - scipy
+  - h5py
+  # additionally, include these deps
+  - ipywidgets
+  - matplotlib
+  - ipympl
+  - jupyterlab
+  - jupyterlab-myst
+  - 'nodejs>=20,<21'
+  - mystmd

index.md

@@ -0,0 +1,34 @@
+---
+title: 'Quickstart Template for Elemental Microscopy'
+short_title: EM Quickstart
+numbering:
+  heading_2: false
+---
+
++++ {"part": "abstract"} 
+
+Add your abstract here.
+Avoid complicated equations / citations here, for crossref compatibility.
+
++++
+
+
++++{"part":"epigraph"}
+:::{warning} Pre-print
+This article has not yet been peer-reviewed.  
+_Updated 2024 August 27_
+:::
+
++++
+
++++ {"part": "acknowledgements"} 
+
+Add your acknowledgments, if any, here.
+
++++
+
++++ {"part": "competing interests"} 
+## Competing Interests
+
+Add your competing interests, if any, here.
++++

myst.yml

@@ -1,43 +1,95 @@
+# See docs at: https://mystmd.org/guide/frontmatter
 version: 1
 project:
-  title: 'Deep Learning Applications in Microscopy: Segmentation and Tracking'
-  description: ''
+  id: msa-em-change-this-to-repo-name-followed-by-the-number-1
+  title: Elemental Microscopy Quickstart
+  description: A minimal repository to be used as quickstart for the Elemental Microscopy journal.
+  short_title: EM Quickstart
+  keywords:
+    - Keyword One
+    - Keyword Two
+    - Spell Out Acronyms
+  github: https://github.com/msa-em/change-this-to-repo-name
+  jupyter: true
+  #  jupyter:
+  #    binder:
+  #      url: https://y2j74k9mn0bz.curvenote.dev/services/binder/
+  #      repo: msa-em/change-this-to-repo-name
+  #  jupyter:
+  #    server:
+  #      url: 'http://localhost:8888'
+  #      token: '512ac78f14e1141db1fac17e8b4099c1e5bc7d589518b38c'
+  open_access: true
+  license: CC-BY-4.0
+  banner: banner.png
+  thumbnail: thumbnail.webp
+  date: 2024-08-27
+  history:
+    submitted: 2023-08-27
+    published: 2024-08-27
+  requirements:
+    - 'environment.yml'
+  resources:
+    - 'notebooks/**/*'
+  references:
+    mystmd: https://mystmd.org/guide
+  exports:
+    - format: meca
+  exclude:
+    - README.md
+    - 'curvenote-export/*'
   authors:
-    - userId: PuMpaY9vxJXq7MgyOn06KAJjJFk1
-      nameParsed:
-        literal: Yifei Duan
-        given: Yifei
-        family: Duan
-      name: Yifei Duan
-      corresponding: false
-      roles: []
-      affiliations: []
-      id: contributors-generated-uid-0
-    - userId: eQLn8OuKA6P0tnqqXpwbKjwbFNT2
-      nameParsed:
-        literal: Yifan Duan
-        given: Yifan
-        family: Duan
-      name: Yifan Duan
-      corresponding: false
-      roles: []
-      affiliations: []
-      id: contributors-generated-uid-1
-  affiliations:
-    - id: 24b97dfc-b244-4100-9c61-08dd5654fa58
-      name: 24b97dfc-b244-4100-9c61-08dd5654fa58
-    - id: 7d4aefe9-595b-44a7-8f83-003fe208d7cf
-      name: 7d4aefe9-595b-44a7-8f83-003fe208d7cf
-  id: 23XJ7d092W52UYjknN3G
-  remote: 23XJ7d092W52UYjknN3G
+    - id: cophus
+      name: Colin Ophus
+      corresponding: true
+      email: [email protected]
+      orcid: 0000-0003-2348-8558
+      affiliations:
+        - id: ncem
+          department: National Center for Electron Microscopy, Molecular Foundry
+          institution: Lawrence Berkeley National Laboratory
+          address: 1 Cyclotron Road, Berkeley, CA, USA, 94720
+          ror: 02jbv0t02
+      roles:
+        - Conceptualization
+        - Funding acquisition
+        - Project administration
+        - Supervision
+        - Visualization
+        - Writing - original draft
+    - id: garnavides
+      name: Georgios Varnavides
+      email: [email protected]
+      orcid: 0000-0001-8338-3323
+      affiliations:
+        - id: miller
+          department: Miller Institute for Basic Research in Science
+          institution: University of California, Berkeley
+          address: 468 Donner Lab, Berkeley, CA, USA, 94720
+          ror: 01an7q238
+      roles:
+        - Conceptualization
+        - Software
+        - Validation
+        - Visualization
+        - Writing - original draft
+  funding:
+    - statement: We thank the Microscopy Society of America for sponsoring this project.
+      recipients:
+        - cophus
+        - garnavides
+    - statement: Work at the Molecular Foundry was supported by the Office of Science, Office of Basic Energy Sciences, of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231.
+      id: DE-AC02-05CH11231
+      sources:
+        - name: Office of Science, Office of Basic Energy Sciences, of the U.S. Department of Energy
+      recipients:
+        - cophus
+  abbreviations:
+    4D-STEM: four dimensional scanning transmission electron microscopy
+    FFT: fast Fourier transform
+    HAADF: high angle annular dark field
+    HRTEM: high resolution transmission electron microscopy
+    M&M: Microscopy and Microanalysis
+    STEM: scanning transmission electron microscopy
 site:
-  title: 'Deep Learning Applications in Microscopy: Segmentation and Tracking'
-  options:
-    logo_text: 'Deep Learning Applications in Microscopy: Segmentation and Tracking'
-  nav:
-    - title: 'Deep Learning Applications in Microscopy: Segmentation and Tracking'
-      url: /deep-learning-applications-in-microscopy-segmentat
-  actions:
-    - title: Learn More
-      url: https://curvenote.com/docs/web
-  domains: []
+  template: book-theme