From 42ddcb5fccd418cbd608a905245e1ab9f2ca18c9 Mon Sep 17 00:00:00 2001 From: Drew Yang Date: Wed, 16 Apr 2025 12:41:03 -0500 Subject: [PATCH 1/2] =?UTF-8?q?feat:=20=E2=9C=A8=20update=20url=20referenc?= =?UTF-8?q?e=20from=20datajoint.com/docs/=20to=20docs.datajoint.com?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- README.md | 14 +++++------ docker-compose.yaml | 2 +- src/additional-resources.md | 32 ++++++++---------------- src/elements/management/dissemination.md | 2 +- src/partnerships/dandi.md | 4 +-- src/partnerships/facemap.md | 4 +-- src/partnerships/nwb.md | 4 +-- src/partnerships/openephysgui.md | 2 +- src/partnerships/suite2p.md | 4 +-- 9 files changed, 28 insertions(+), 40 deletions(-) diff --git a/README.md b/README.md index 8db4678b..e82f9ea7 100644 --- a/README.md +++ b/README.md @@ -1,7 +1,6 @@ # DataJoint Documentation -This is the home for DataJoint software documentation as hosted at https://datajoint.com/docs - +This is the home for DataJoint software documentation as hosted at https://docs.datajoint.com ## VSCode Linter Extensions and Settings The following extensions were used in developing these docs, with the corresponding @@ -39,7 +38,7 @@ Then install the required packages: pip install -r pip_requirements.txt ``` -Run mkdocs at: http://127.0.0.1:8000/docs/ +Run mkdocs at: http://127.0.0.1:8000/ ```bash # It will automatically reload the docs when changes are made mkdocs serve --config-file ./mkdocs.yaml @@ -57,7 +56,7 @@ Then run the following: MODE="LIVE" docker compose up --build ``` -Navigate to http://127.0.0.1:8000/docs/ to preview the changes. +Navigate to http://127.0.0.1:8000/ to preview the changes. This setup supports live-reloading so all that is needed is to save the markdown files and/or `mkdocs.yaml` file to trigger a reload. @@ -77,10 +76,9 @@ INFO - Doc file 'index.md' contains an unrecognized relative link './core/da - You hit `datajoint.com/*` on your browser - It'll bring you to the reverse proxy server first, that you wouldn't notice - when your URL ends with: - - `/` is the company page - - `/docs/` is the landing/navigation page hosted by datajoint/datajoint-docs's github pages - - `/docs/core/datajoint-python/` is the actual docs site hosted by datajoint/datajoint-python's github pages - - `/docs/elements/element-*/` is the actual docs site hosted by each element's github pages + - `/` is the landing/navigation page hosted by datajoint/datajoint-docs's github pages + - `/core/datajoint-python/` is the actual docs site hosted by datajoint/datajoint-python's github pages + - `/elements/element-*/` is the actual docs site hosted by each element's github pages ```log diff --git a/docker-compose.yaml b/docker-compose.yaml index 4631a3f6..3ffd42f3 100644 --- a/docker-compose.yaml +++ b/docker-compose.yaml @@ -1,6 +1,6 @@ # MODE="LIVE|BUILD" docker compose up --build # -# Navigate to http://localhost/docs/ +# Navigate to http://localhost:8000/ services: docs: # image: datajoint/datajoint-docs diff --git a/src/additional-resources.md b/src/additional-resources.md index 6f8c1d44..8bcff22c 100644 --- a/src/additional-resources.md +++ b/src/additional-resources.md @@ -12,7 +12,7 @@ A collection of additional open-source tools for building and operating scientif A MATLAB client for defining, operating, and querying data pipelines. - :octicons-arrow-right-24: [Legacy docs](https://docs.datajoint.org/matlab/) | + :octicons-arrow-right-24: [Legacy docs](https://datajoint.github.io/datajoint-docs-original/matlab/) | [Source code](https://github.com/datajoint/datajoint-matlab) - :fontawesome-solid-flask:{ .lg .middle } **DataJoint Pharus** @@ -21,7 +21,7 @@ A collection of additional open-source tools for building and operating scientif A REST API server for interacting with DataJoint pipelines. - :octicons-arrow-right-24: [Docs](https://datajoint.com/docs/core/pharus) | + :octicons-arrow-right-24: [Docs](https://docs.datajoint.com/core/pharus) | [Source code](https://github.com/datajoint/pharus/) @@ -36,8 +36,7 @@ A collection of additional open-source tools for building and operating scientif A browser-based graphical user interface for data entry and navigation. - :octicons-arrow-right-24: [Legacy - docs](https://datajoint.com/docs/core/datajoint-labbook/) | + :octicons-arrow-right-24: [Legacy docs](https://datajoint.github.io/datajoint-labbook/) | [Source code](https://github.com/datajoint/datajoint-labbook/) - :fontawesome-brands-chrome:{ .lg .middle } **DataJoint SciViz** @@ -46,7 +45,7 @@ A collection of additional open-source tools for building and operating scientif A framework for making low-code web apps for data visualization. - :octicons-arrow-right-24: [Legacy docs](https://datajoint.com/docs/core/sci-viz/) | + :octicons-arrow-right-24: [Docs](https://docs.datajoint.com/core/sci-viz/) | [Source code](https://github.com/datajoint/sci-viz) @@ -78,8 +77,7 @@ graph --- MySQL server configured to work with DataJoint. - :octicons-arrow-right-24: [Docker - image](https://hub.docker.com/r/datajoint/mysql) | + :octicons-arrow-right-24: [Docker image](https://hub.docker.com/r/datajoint/mysql) | [Source code](https://github.com/datajoint/mysql-docker) - :fontawesome-brands-docker:{ .lg .middle } **datajoint/miniconda3** @@ -88,8 +86,7 @@ graph Minimal Python Docker image with [conda](https://docs.conda.io/en/latest/). - :octicons-arrow-right-24: [Docker - image](https://hub.docker.com/r/datajoint/miniconda3) | + :octicons-arrow-right-24: [Docker image](https://hub.docker.com/r/datajoint/miniconda3) | [Legacy docs](https://datajoint.github.io/miniconda3-docker/) | [Source code](https://github.com/datajoint/miniconda3-docker) @@ -99,8 +96,7 @@ graph Minimal base Docker image with DataJoint Python dependencies installed. - :octicons-arrow-right-24: [Docker - image](https://hub.docker.com/r/datajoint/djbase) | + :octicons-arrow-right-24: [Docker image](https://hub.docker.com/r/datajoint/djbase) | [Legacy docs](https://datajoint.github.io/djbase-docker/) | [Source code](https://github.com/datajoint/djbase-docker) @@ -110,8 +106,7 @@ graph Docker image for running tests related to DataJoint Python. - :octicons-arrow-right-24: [Docker - image](https://hub.docker.com/r/datajoint/djtest) | + :octicons-arrow-right-24: [Docker image](https://hub.docker.com/r/datajoint/djtest) | [Legacy docs](https://datajoint.github.io/djtest-docker/) | [Source code](https://github.com/datajoint/djtest-docker) @@ -121,8 +116,7 @@ graph Official DataJoint Docker image. - :octicons-arrow-right-24: [Docker - image](https://hub.docker.com/r/datajoint/datajoint) | + :octicons-arrow-right-24: [Docker image](https://hub.docker.com/r/datajoint/datajoint) | [Source code](https://github.com/datajoint/datajoint-python) - :fontawesome-brands-docker:{ .lg .middle } **datajoint/djlab** @@ -131,9 +125,7 @@ graph Docker image optimized for running a JupyterLab environment with DataJoint Python. - :octicons-arrow-right-24: [Docker - image](https://hub.docker.com/r/datajoint/djlab) | - [Legacy docs](https://datajoint.github.io/djlab-docker/) | + :octicons-arrow-right-24: [Docker image](https://hub.docker.com/r/datajoint/djlab) | [Source code](https://github.com/datajoint/djlab-docker) - :fontawesome-brands-docker:{ .lg .middle } **datajoint/djlabhub** @@ -143,9 +135,7 @@ graph Docker image optimized for deploying to JupyterHub a JupyterLab environment with DataJoint Python. - :octicons-arrow-right-24: [Docker - image](https://hub.docker.com/r/datajoint/djlabhub) | - [Legacy docs](https://datajoint.github.io/djlabhub-docker/) | + :octicons-arrow-right-24: [Docker image](https://hub.docker.com/r/datajoint/djlabhub) | [Source code](https://github.com/datajoint/djlabhub-docker) diff --git a/src/elements/management/dissemination.md b/src/elements/management/dissemination.md index f0759cbc..56390481 100644 --- a/src/elements/management/dissemination.md +++ b/src/elements/management/dissemination.md @@ -5,7 +5,7 @@ We conduct activities to disseminate Resource components for adoption in diverse neuroscience labs. These activities include -- A central [website](https://datajoint.com/docs/elements/) for the Resource. +- A central [website](https://docs.datajoint.com/elements/) for the Resource. - [Conference talks, presentations, and workshops](../../support-events.md) - Publications in peer-reviewed journals - White papers posted on internet resources and websites diff --git a/src/partnerships/dandi.md b/src/partnerships/dandi.md index cb63a721..5867804b 100644 --- a/src/partnerships/dandi.md +++ b/src/partnerships/dandi.md @@ -20,9 +20,9 @@ integration and interoperability across the two ecosystems. ### DataJoint -**DataJoint Elements** — https://datajoint.com/docs/elements/ — is a collection of +**DataJoint Elements** — https://docs.datajoint.com/elements/ — is a collection of open-source reference database schemas and analysis workflows for neurophysiology - experiments, supported by **DataJoint** — https://datajoint.com/docs/core/ — an + experiments, supported by **DataJoint** — https://docs.datajoint.com/core/ — an open-source software framework. The project is funded by the NIH grant U24 NS116470 and led by Dr. Dimitri Yatsenko. diff --git a/src/partnerships/facemap.md b/src/partnerships/facemap.md index de7229d4..2d36fe5d 100644 --- a/src/partnerships/facemap.md +++ b/src/partnerships/facemap.md @@ -20,9 +20,9 @@ across the two ecosystems. ### DataJoint -**DataJoint Elements** — https://datajoint.com/docs/elements/ — is a collection of +**DataJoint Elements** — https://docs.datajoint.com/elements/ — is a collection of open-source reference database schemas and analysis workflows for neurophysiology - experiments, supported by **DataJoint** — https://datajoint.com/docs/core/ — an + experiments, supported by **DataJoint** — https://docs.datajoint.com/core/ — an open-source software framework. The project is funded by the NIH grant U24 NS116470 and led by Dr. Dimitri Yatsenko. diff --git a/src/partnerships/nwb.md b/src/partnerships/nwb.md index 5be1cad8..1c06263c 100644 --- a/src/partnerships/nwb.md +++ b/src/partnerships/nwb.md @@ -20,9 +20,9 @@ ### DataJoint -**DataJoint Elements** — https://datajoint.com/docs/elements/ — is a collection of +**DataJoint Elements** — https://docs.datajoint.com/elements/ — is a collection of open-source reference database schemas and analysis workflows for neurophysiology - experiments, supported by **DataJoint** — https://datajoint.com/docs/core/ — an + experiments, supported by **DataJoint** — https://docs.datajoint.com/core/ — an open-source software framework. The project is funded by the NIH grant U24 NS116470 and led by Dr. Dimitri Yatsenko. diff --git a/src/partnerships/openephysgui.md b/src/partnerships/openephysgui.md index 0bd151d9..1fe71f5f 100644 --- a/src/partnerships/openephysgui.md +++ b/src/partnerships/openephysgui.md @@ -16,7 +16,7 @@ ### DataJoint -**DataJoint Elements** — https://datajoint.com/docs/elements/ — is a collection of open-source reference database schemas and analysis workflows for neurophysiology experiments, supported by **DataJoint Core** — https://datajoint.com/docs/core/ — an open-source software framework. The project is funded by the NIH grant U24 NS116470 and led by Dr. Dimitri Yatsenko. +**DataJoint Elements** — https://docs.datajoint.com/elements/ — is a collection of open-source reference database schemas and analysis workflows for neurophysiology experiments, supported by **DataJoint Core** — https://docs.datajoint.com/core/ — an open-source software framework. The project is funded by the NIH grant U24 NS116470 and led by Dr. Dimitri Yatsenko. The principal developer of DataJoint Elements and DataJoint Core is the company DataJoint — https://datajoint.com. diff --git a/src/partnerships/suite2p.md b/src/partnerships/suite2p.md index f05cd5da..dc04ab34 100644 --- a/src/partnerships/suite2p.md +++ b/src/partnerships/suite2p.md @@ -20,9 +20,9 @@ ### DataJoint -**DataJoint Elements** — https://datajoint.com/docs/elements/ — is a collection of +**DataJoint Elements** — https://docs.datajoint.com/elements/ — is a collection of open-source reference database schemas and analysis workflows for neurophysiology - experiments, supported by **DataJoint** — https://datajoint.com/docs/core/ — an + experiments, supported by **DataJoint** — https://docs.datajoint.com/core/ — an open-source software framework. The project is funded by the NIH grant U24 NS116470 and led by Dr. Dimitri Yatsenko. From 90bdc8f8926aa94eeb9c0fc56994bb77e4734044 Mon Sep 17 00:00:00 2001 From: Drew Yang Date: Wed, 16 Apr 2025 13:59:09 -0500 Subject: [PATCH 2/2] =?UTF-8?q?fix:=20=F0=9F=90=9B=20fix=20mermaid=20chart?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- mkdocs.yaml | 3 ++- pip_requirements.txt | 3 ++- src/elements/user-guide.md | 35 ++++++++++++++--------------------- 3 files changed, 18 insertions(+), 23 deletions(-) diff --git a/mkdocs.yaml b/mkdocs.yaml index 6ad5dd1e..48067e28 100644 --- a/mkdocs.yaml +++ b/mkdocs.yaml @@ -71,6 +71,7 @@ theme: name: Switch to light mode plugins: - search + - mermaid2 - section-index # There is no welcome.md anymore # - redirects: @@ -96,7 +97,7 @@ markdown_extensions: custom_fences: - name: mermaid class: mermaid - format: !!python/name:pymdownx.superfences.fence_code_format + format: !!python/name:mermaid2.fence_mermaid_custom - pymdownx.tabbed: alternate_style: true - footnotes diff --git a/pip_requirements.txt b/pip_requirements.txt index c321401c..0f1a2e2b 100644 --- a/pip_requirements.txt +++ b/pip_requirements.txt @@ -4,4 +4,5 @@ mkdocs-exclude mdx_truly_sane_lists mkdocs-pymdownx-material-extras pymdown-extensions -mkdocs-section-index \ No newline at end of file +mkdocs-section-index +mkdocs-mermaid2-plugin \ No newline at end of file diff --git a/src/elements/user-guide.md b/src/elements/user-guide.md index 86d979d9..b76ea1d2 100644 --- a/src/elements/user-guide.md +++ b/src/elements/user-guide.md @@ -42,27 +42,20 @@ This diagram describes the general components for a local DataJoint environment. ```mermaid flowchart LR - py_interp -->|DataJoint| db_server[("Database Server\n(e.g., MySQL)")] - subgraph conda["Conda environment"] - direction TB - py_interp[Python Interpreter] - end - subgraph empty1[" "] %% Empty subgraphs prevent overlapping titles - direction TB - style empty1 fill:none, stroke-dasharray: 0 1 - conda - end - subgraph term["Terminal or Jupyter Notebook"] - direction TB - empty1 - end - subgraph empty2[" "] %% Empty subgraphs prevent overlapping titles - direction TB - style empty2 fill:none, stroke-dasharray: 0 1 - term - end - class py_interp,conda,term,ide,db_server,DataJoint boxes; - classDef boxes fill:#ddd, stroke:#333; + %% Nodes + py_interp["Python Interpreter"] + db_server["Database Server
(e.g., MySQL)"] + conda_env["Conda Environment"] + terminal["Terminal or Jupyter Notebook"] + + %% Edges + py_interp -->|DataJoint| db_server + terminal --> conda_env + conda_env --> py_interp + + %% Styling + classDef boxes fill:#ddd,stroke:#333; + class py_interp,db_server,conda_env,terminal boxes; ``` ### Python