diff --git a/.github/workflows/sync_project.yml b/.github/workflows/sync_project.yml index 29fc7a0..76df681 100644 --- a/.github/workflows/sync_project.yml +++ b/.github/workflows/sync_project.yml @@ -1,13 +1,16 @@ name: cookietemple sync -on: [push] +on: + schedule: + - cron: '0 1 * * *' # 1 am UTC + workflow_dispatch: jobs: build: runs-on: ubuntu-latest steps: - name: Setup Python - uses: actions/setup-python@v1 + uses: actions/setup-python@v2.1.4 with: python-version: 3.8 @@ -17,14 +20,15 @@ jobs: - uses: actions/checkout@v2 with: fetch-depth: 0 + token: '${{ secrets.CT_SYNC_TOKEN }}' name: Check out source-code repository - - uses: oleksiyrudenko/gha-git-credentials@v1 + - uses: oleksiyrudenko/gha-git-credentials@v2 with: name: 'zethson' email: 'lukas.heumos@posteo.net' actor: 'zethson' - token: '${{ secrets.CT_SYNC_TOKEN}}' + token: '${{ secrets.CT_SYNC_TOKEN }}' - name: Sync project run: cookietemple sync . ${{ secrets.CT_SYNC_TOKEN }} zethson diff --git a/cookietemple.cfg b/cookietemple.cfg index d08859f..314ae5f 100644 --- a/cookietemple.cfg +++ b/cookietemple.cfg @@ -3,6 +3,7 @@ current_version = 0.1.0 [bumpversion_files_whitelisted] setup_file = setup.py +dot_cookietemple = .cookietemple.yml [bumpversion_files_blacklisted] @@ -10,4 +11,6 @@ setup_file = setup.py ct_sync_level = minor [sync_files_blacklisted] - +changelog = CHANGELOG.rst +requirements = requirements.txt +requirements_dev = requirements_dev.txt diff --git a/docs/requirements.txt b/docs/requirements.txt index 1eaea77..4a4c2b3 100644 --- a/docs/requirements.txt +++ b/docs/requirements.txt @@ -1,4 +1,4 @@ -Sphinx==2.4.4 -sphinx_rtd_theme==0.5.0 +Sphinx==3.5.2 +sphinx_rtd_theme==0.5.1 sphinx-automodapi==0.13 -r ../requirements.txt diff --git a/mlf_core_website/basic/routes.py b/mlf_core_website/basic/routes.py index b6a5c9e..b5eed99 100644 --- a/mlf_core_website/basic/routes.py +++ b/mlf_core_website/basic/routes.py @@ -31,3 +31,8 @@ def about(): @bp.route('/code_of_conduct') def code_of_conduct(): return render_template('code_of_conduct.html') + + +@bp.route('/projects') +def projects(): + return render_template('projects.html') diff --git a/mlf_core_website/static/assets/css/mlf_core.css b/mlf_core_website/static/assets/css/mlf_core.css index 30e51f1..dd2aed1 100644 --- a/mlf_core_website/static/assets/css/mlf_core.css +++ b/mlf_core_website/static/assets/css/mlf_core.css @@ -517,7 +517,7 @@ Based on https://codepen.io/wintr/pen/beBJBb */ height: 42px; box-shadow: 2px 3px 4px rgba(51,51,51, 0.4); -webkit-transition: background 0.1s; - transition: background 0.1s; + transition: transform .5s; /* Animation */ } .list-switch a .label { margin-right: 10px; @@ -526,7 +526,8 @@ Based on https://codepen.io/wintr/pen/beBJBb */ border-top: 1px solid #292929; } .list-switch a:hover, .list-switch a:active, .list-switch a:focus { - background-color: #555; + background-color: #2d6995; + transform: scale(1.1); } @media (min-width: 992px) { .list-switch.left a { @@ -554,7 +555,7 @@ Based on https://codepen.io/wintr/pen/beBJBb */ right: -42px; } .list-switch.left a:hover:before, .list-switch.left a:active:before, .list-switch.left a:focus:before { - border-right-color: #555; + border-right-color: #2d6995; } .list-switch.right a:hover:before, .list-switch.right a:active:before, .list-switch.right a:focus:before { border-left-color: #555; diff --git a/mlf_core_website/static/assets/img/about_core_team/philipp.jpg b/mlf_core_website/static/assets/img/about_core_team/philipp.jpg new file mode 100644 index 0000000..95ae3ed Binary files /dev/null and b/mlf_core_website/static/assets/img/about_core_team/philipp.jpg differ diff --git a/mlf_core_website/static/assets/img/background_header/red_blue.png b/mlf_core_website/static/assets/img/background_header/red_blue.png new file mode 100644 index 0000000..dc5a12e Binary files /dev/null and b/mlf_core_website/static/assets/img/background_header/red_blue.png differ diff --git a/mlf_core_website/static/assets/img/index_gifs/bump_ML.gif b/mlf_core_website/static/assets/img/index_gifs/bump_ML.gif new file mode 100644 index 0000000..4e38c58 Binary files /dev/null and b/mlf_core_website/static/assets/img/index_gifs/bump_ML.gif differ diff --git a/mlf_core_website/static/assets/img/index_gifs/config_ML.gif b/mlf_core_website/static/assets/img/index_gifs/config_ML.gif new file mode 100644 index 0000000..53358de Binary files /dev/null and b/mlf_core_website/static/assets/img/index_gifs/config_ML.gif differ diff --git a/mlf_core_website/static/assets/img/index_gifs/create_ML.gif b/mlf_core_website/static/assets/img/index_gifs/create_ML.gif new file mode 100644 index 0000000..0ad54bf Binary files /dev/null and b/mlf_core_website/static/assets/img/index_gifs/create_ML.gif differ diff --git a/mlf_core_website/static/assets/img/index_gifs/lint_ML.gif b/mlf_core_website/static/assets/img/index_gifs/lint_ML.gif new file mode 100644 index 0000000..164242e Binary files /dev/null and b/mlf_core_website/static/assets/img/index_gifs/lint_ML.gif differ diff --git a/mlf_core_website/static/assets/img/index_gifs/sync_ML.gif b/mlf_core_website/static/assets/img/index_gifs/sync_ML.gif new file mode 100644 index 0000000..c6f0315 Binary files /dev/null and b/mlf_core_website/static/assets/img/index_gifs/sync_ML.gif differ diff --git a/mlf_core_website/static/assets/img/logo/mlf_core_transparent_cropped.png b/mlf_core_website/static/assets/img/logo/mlf_core_transparent_cropped.png deleted file mode 100644 index 0c2bd67..0000000 Binary files a/mlf_core_website/static/assets/img/logo/mlf_core_transparent_cropped.png and /dev/null differ diff --git a/mlf_core_website/static/assets/img/logo/mlf_core_transparent_cropped.svg b/mlf_core_website/static/assets/img/logo/mlf_core_transparent_cropped.svg new file mode 100644 index 0000000..295d937 --- /dev/null +++ b/mlf_core_website/static/assets/img/logo/mlf_core_transparent_cropped.svg @@ -0,0 +1,4301 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/mlf_core_website/templates/LICENSE b/mlf_core_website/templates/LICENSE new file mode 100644 index 0000000..fe3f3a7 --- /dev/null +++ b/mlf_core_website/templates/LICENSE @@ -0,0 +1,22 @@ +Copyright (c) 2020-2021 mlf-core +Copyright (c) 2018 nf-core + +MIT License + +Permission is hereby granted, free of charge, to any person obtaining a copy +of this software and associated documentation files (the "Software"), to deal +in the Software without restriction, including without limitation the rights +to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +copies of the Software, and to permit persons to whom the Software is +furnished to do so, subject to the following conditions: + +The above copyright notice and this permission notice shall be included in all +copies or substantial portions of the Software. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE +SOFTWARE. diff --git a/mlf_core_website/templates/about.html b/mlf_core_website/templates/about.html index 51facf0..cd9f48e 100644 --- a/mlf_core_website/templates/about.html +++ b/mlf_core_website/templates/about.html @@ -9,6 +9,7 @@ + @@ -23,149 +24,335 @@ + @@ -23,6 +24,7 @@ + + + + @@ -39,47 +164,42 @@
-
- - - -

- Deterministic machine learning project templates based on MLflow.

-
- View Templates -
+
+
+
+

Deterministic machine learning project templates + based on MLflow.

+
+ +
-
-
+

For users

Highly customizable, ready-to-use templates for project setup in seconds.

+

For developers

-

A community to build standardized, well-designed templates to accelerate your workflow.

+

A community to build standardized and deterministic machine learning models.

+

For companies

Standardize your workflow, group experiments, track parameters and metrics and benefit from fully reproducible results.

-

- -

+

-
- -
-

mlf-core is an open-source effort to facilitate deterministic machine learning and enable best practices.

-
- +

Hey

+

Hey

@@ -87,7 +207,7 @@

For companies

Frameworks
-

mlf-core provides deterministic, standardized templates for several machine learning frameworks.

+

mlf-core provides deterministic and standardized templates for several machine learning frameworks.

@@ -140,25 +260,43 @@
Community
-
-
+
+
-
- -
- -{#

More videos coming soon..

#} -
-
+
@@ -166,9 +304,11 @@
Community

Get started in minutes

-

mlf-core currently offers support for Linux and MacOS.

-

It comes with a bunch of useful commands to make your life during development easier.

-

Make sure to check out the documentation for details.

+

Make sure to check out the documentation for details. +

+ + +
diff --git a/mlf_core_website/templates/projects.html b/mlf_core_website/templates/projects.html new file mode 100644 index 0000000..9cea0a0 --- /dev/null +++ b/mlf_core_website/templates/projects.html @@ -0,0 +1,332 @@ + + + + + + Projects of mlf-core + + + + + + + + + + + + + + + + + + + + + + + + + +{% include 'header.html' %} + +
+
+
+

Projects

+
+
+ +
+ +

mlf-core projects

+

mlf-core aims to be a tool for the complete machine learning cycle. + Below are some of those projects listed, that were created and developed using mlf-core. If would like to see your project listed here as well, + create an issue at the mlf-core + repository.

+ + + + + +
+
+
+

+ + mlf-core mlflow-pytorch + +

+

+ mlflow + pytorch +

+

Segmentation of liver computed tomography images with a UNET.

+

+ + View on GitHub +   +

+ + + +
+
+ +
+
+

+ + mlf-core sc-autoencoder + +

+

+ mlflow + tensorflow +

+

An autoencoder for single cell data with fully reproducible mlf-core Tensorflow model.

+

+ + View on GitHub + +

+ + + +
+
+ +
+
+

+ + mlf-core lcep + +

+

+ mlflow + xgboost +

+

Classify cancerous and benign liver samples from gene expression data with fully deterministic machine learning + model based on XGBoost and MLflow

+

+ + View on GitHub +   +

+ + + +
+
+
+
+
+ +{% include 'footer.html' %} + + + diff --git a/mlf_core_website/templates/templates.html b/mlf_core_website/templates/templates.html index 1220ae3..d8e1a4d 100644 --- a/mlf_core_website/templates/templates.html +++ b/mlf_core_website/templates/templates.html @@ -9,6 +9,7 @@ + @@ -30,24 +31,188 @@ gtag('js', new Date()); gtag('config', 'UA-68098153-2'); + + {% include 'header.html' %}
-
-
-

Templates

-

Browse the 4 templates that are currently available as part of mlf-core.

+
+
+

Templates

+
- -
-

Available Templates

-

Can you think of another template that would fit in well? +

Browse the 4 mlf-core templates that are currently available. Can you think of another template that would fit in well? Let us know!

diff --git a/requirements.txt b/requirements.txt index 73f1b7d..3683932 100644 --- a/requirements.txt +++ b/requirements.txt @@ -1,4 +1,4 @@ Click==7.1.2 Flask==1.1.2 -gevent==20.9.0 +gevent==21.1.2 diff --git a/requirements_dev.txt b/requirements_dev.txt index 5c20495..dd748a1 100644 --- a/requirements_dev.txt +++ b/requirements_dev.txt @@ -1,12 +1,12 @@ pip>=20.2.2 wheel>=0.35.1 -watchdog==0.10.3 +watchdog==2.0.2 flake8==3.8.4 -tox==3.20.1 -coverage==5.3 -Sphinx==3.2.1 -twine==3.2.0 -pytest==6.1.1 -pytest-runner==5.2 -pytest-mock==3.3.1 +tox==3.23.0 +coverage==5.5 +Sphinx==3.5.2 +twine==3.3.0 +pytest==6.2.2 +pytest-runner==5.3.0 +pytest-mock==3.5.1 -r requirements.txt