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fix(git): rename master to main
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Signed-off-by: Cameron Smith <[email protected]>
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cameronraysmith committed Jan 3, 2024
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2 changes: 1 addition & 1 deletion .example.env
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Expand Up @@ -61,7 +61,7 @@ CONTAINER_BUILDER=podman # path to container management executable
GITHUB_USERNAME=username # github username associated to uploading startup scripts as github gists
GITHUB_ORG_NAME=pinellolab # name of the github org or user containing the github repository with code for development
GITHUB_REPO_NAME=pyrovelocity # name of a github repository with a conda environment yaml file
GITHUB_BRANCH_NAME=master # name of github repository branch to checkout
GITHUB_BRANCH_NAME=main # name of github repository branch to checkout
POD_DISK_SIZE=400Gi # size of the PVC to mount to the devpod
POD_ACCELERATOR_TYPE=nvidia-tesla-t4 # cluster-specific node selector for accelerator type | nvidia-l4 | nvidia-tesla-a100
POD_MIN_CPU=16 # cpu resource request for kubernetes pod
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3 changes: 2 additions & 1 deletion .vscode/settings.json
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Expand Up @@ -24,5 +24,6 @@
"terminal.integrated.scrollback": 100000,
"terminal.integrated.persistentSessionScrollback": 100000,
"editor.fontSize": 16,
"terminal.integrated.fontSize": 14
"terminal.integrated.fontSize": 14,
"julia.environmentPath": "/Users/crs58/projects/pyrovelocity-01032024"
}
20 changes: 10 additions & 10 deletions README.md
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Expand Up @@ -2,14 +2,14 @@

<div align="center">

<img src="https://raw.githubusercontent.com/pinellolab/pyrovelocity/master/docs/_static/logo.png" alt="Pyro-Velocity logo" width="300" role="img">
<img src="https://raw.githubusercontent.com/pinellolab/pyrovelocity/main/docs/_static/logo.png" alt="Pyro-Velocity logo" width="300" role="img">

| | |
| ------- | ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
| CI/CD | [![CID](https://github.com/pinellolab/pyrovelocity/actions/workflows/cid.yaml/badge.svg?branch=master)](https://github.com/pinellolab/pyrovelocity/actions/workflows/cid.yaml) [![CML](https://github.com/pinellolab/pyrovelocity/actions/workflows/cml.yml/badge.svg)](https://github.com/pinellolab/pyrovelocity/actions/workflows/cml.yml) [![pre-commit.ci status](https://results.pre-commit.ci/badge/github/pinellolab/pyrovelocity/master.svg)](https://results.pre-commit.ci/latest/github/pinellolab/pyrovelocity/master) |
| CI/CD | [![CID](https://github.com/pinellolab/pyrovelocity/actions/workflows/cid.yaml/badge.svg?branch=master)](https://github.com/pinellolab/pyrovelocity/actions/workflows/cid.yaml) [![CML](https://github.com/pinellolab/pyrovelocity/actions/workflows/cml.yml/badge.svg)](https://github.com/pinellolab/pyrovelocity/actions/workflows/cml.yml) [![pre-commit.ci status](https://results.pre-commit.ci/badge/github/pinellolab/pyrovelocity/main.svg)](https://results.pre-commit.ci/latest/github/pinellolab/pyrovelocity/master) |
| Docs | [![GitHub Pages](https://img.shields.io/github/deployments/pinellolab/pyrovelocity/github-pages?logo=github&label=Docs)](https://pinellolab.github.io/pyrovelocity) [![Preprint](https://img.shields.io/badge/doi-10.1101/2022.09.12.507691v2-B31B1B)](https://doi.org/10.1101/2022.09.12.507691) |
| Package | [![PyPI - Version](https://img.shields.io/pypi/v/pyrovelocity.svg?logo=pypi&label=PyPI&logoColor=gold)](https://pypi.org/project/pyrovelocity/) [![PyPI - Python Version](https://img.shields.io/pypi/pyversions/pyrovelocity.svg?logo=python&label=Python&logoColor=gold)](https://pypi.org/project/pyrovelocity/) [![Docker iamge](https://img.shields.io/badge/docker-image-blue?logo=docker)](https://github.com/pinellolab/pyrovelocity/pkgs/container/pyrovelocity) |
| Meta | [![codecov](https://codecov.io/gh/pinellolab/pyrovelocity/branch/master/graph/badge.svg)](https://codecov.io/gh/pinellolab/pyrovelocity) [![code style - Black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black) [![License - MIT](https://img.shields.io/badge/license-AGPL%203-purple)](https://spdx.org/licenses/) [![Tuple](https://img.shields.io/badge/Tuple%20❤️%20OSS-5A67D8?logo=tuple)](https://tuple.app/github-badge) |
| Meta | [![codecov](https://codecov.io/gh/pinellolab/pyrovelocity/branch/main/graph/badge.svg)](https://codecov.io/gh/pinellolab/pyrovelocity) [![code style - Black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black) [![License - MIT](https://img.shields.io/badge/license-AGPL%203-purple)](https://spdx.org/licenses/) [![Tuple](https://img.shields.io/badge/Tuple%20❤️%20OSS-5A67D8?logo=tuple)](https://tuple.app/github-badge) |

</div>

Expand Down Expand Up @@ -266,7 +266,7 @@ biology underlying these cells.
**Vector field with uncertainty**

<!-- ![PBMC vector field uncertainty](docs/source/readme_figure2.png) -->
<img src="https://raw.githubusercontent.com/pinellolab/pyrovelocity/master/docs/source/readme_figure2.png" alt="PBMC vector field uncertainty">
<img src="https://raw.githubusercontent.com/pinellolab/pyrovelocity/main/docs/source/readme_figure2.png" alt="PBMC vector field uncertainty">

These 6 plots from left to right show: 1. cell types, 2. stream plot of
Pyro-velocity vector field based on the posterior mean of 30 posterior
Expand Down Expand Up @@ -300,7 +300,7 @@ Delta, and Epsilon cells.
**Vector field with uncertainty**

<!-- ![Pancreas vector field uncertainty](docs/source/readme_figure3.png) -->
<img src="https://raw.githubusercontent.com/pinellolab/pyrovelocity/master/docs/source/readme_figure3.png" alt="Pancreas vector field uncertainty">
<img src="https://raw.githubusercontent.com/pinellolab/pyrovelocity/main/docs/source/readme_figure3.png" alt="Pancreas vector field uncertainty">

These 6 plots from left to right are showing the same analyses presented
as in the example above.
Expand All @@ -326,14 +326,14 @@ genes using Pearson\'s correlation between denoised spliced expression
and the posterior mean of the recovered shared time across cells.

<!-- ![Pancreas Volcano plot for gene selection](docs/source/readme_figure6.png) -->
<img src="https://raw.githubusercontent.com/pinellolab/pyrovelocity/master/docs/source/readme_figure6.png" alt="Pancreas Volcano plot for gene selection">
<img src="https://raw.githubusercontent.com/pinellolab/pyrovelocity/main/docs/source/readme_figure6.png" alt="Pancreas Volcano plot for gene selection">

For the selected genes, it is possible to explore in depth their
dynamic, using phase portraits, rainbow plots, and UMAP rendering of
denoised splicing gene expression across cells.

<!-- ![Pancreas vector field uncertainty](docs/source/readme_figure7.png) -->
<img src="https://raw.githubusercontent.com/pinellolab/pyrovelocity/master/docs/source/readme_figure7.png" alt="Pancreas vector field uncertainty">
<img src="https://raw.githubusercontent.com/pinellolab/pyrovelocity/main/docs/source/readme_figure7.png" alt="Pancreas vector field uncertainty">

The full example can be reproduced using the
[Pancreas](https://github.com/pinellolab/pyrovelocity/blob/master/docs/source/notebooks/pancreas.ipynb)
Expand All @@ -354,7 +354,7 @@ Below we show the main output generated by Pyro-Velocity analysis.
**Vector field with uncertainty**

<!-- ![LARRY vector field uncertainty](docs/source/readme_figure8.png) -->
<img src="https://raw.githubusercontent.com/pinellolab/pyrovelocity/master/docs/source/readme_figure8.png" alt="LARRY vector field uncertainty">
<img src="https://raw.githubusercontent.com/pinellolab/pyrovelocity/main/docs/source/readme_figure8.png" alt="LARRY vector field uncertainty">

These 5 plots from left to right shows: 1) Cell types, 2) Clone
progression vector field by using centroid of cells belonging to the
Expand All @@ -373,7 +373,7 @@ state-of-the-art method specifically designed for predicting fate
potency based on LARRY data.

<!-- ![Pancreas shared time uncertainty](docs/source/readme_figure9.png) -->
<img src="https://raw.githubusercontent.com/pinellolab/pyrovelocity/master/docs/source/readme_figure9.png" alt="Pancreas shared time uncertainty">
<img src="https://raw.githubusercontent.com/pinellolab/pyrovelocity/main/docs/source/readme_figure9.png" alt="Pancreas shared time uncertainty">

The leftmost figure shows the Cospar fate potency score, the middle
figure shows the average of 30 posterior samples from Pyro-Velocity
Expand All @@ -383,7 +383,7 @@ derived from Cospar, the right figure shows the standard deviation
across posterior samples of shared time.

The full example can be reproduced using the
[LARRY](https://github.com/pinellolab/pyrovelocity/blob/master/docs/source/notebooks/larry.ipynb)
[LARRY](https://github.com/pinellolab/pyrovelocity/blob/main/docs/source/notebooks/larry.ipynb)
jupyter notebook.

# Troubleshooting
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2 changes: 1 addition & 1 deletion app/app.py
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Expand Up @@ -11,7 +11,7 @@

st.set_page_config(
page_title="pyrovelocity report",
page_icon="https://raw.githubusercontent.com/pinellolab/pyrovelocity/master/docs/_static/logo.png",
page_icon="https://raw.githubusercontent.com/pinellolab/pyrovelocity/main/docs/_static/logo.png",
layout="wide",
initial_sidebar_state="auto",
)
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4 changes: 2 additions & 2 deletions app/modules/home.py
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Expand Up @@ -10,10 +10,10 @@
home_markdown_table = """
| | |
| ------- | ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
| CI/CD | [![CI - Test](https://github.com/pinellolab/pyrovelocity/actions/workflows/tests.yml/badge.svg)](https://github.com/pinellolab/pyrovelocity/actions/workflows/tests.yml) [![CML](https://github.com/pinellolab/pyrovelocity/actions/workflows/cml.yml/badge.svg)](https://github.com/pinellolab/pyrovelocity/actions/workflows/cml.yml) [![pre-commit.ci status](https://results.pre-commit.ci/badge/github/pinellolab/pyrovelocity/master.svg)](https://results.pre-commit.ci/latest/github/pinellolab/pyrovelocity/master) |
| CI/CD | [![CI - Test](https://github.com/pinellolab/pyrovelocity/actions/workflows/tests.yml/badge.svg)](https://github.com/pinellolab/pyrovelocity/actions/workflows/tests.yml) [![CML](https://github.com/pinellolab/pyrovelocity/actions/workflows/cml.yml/badge.svg)](https://github.com/pinellolab/pyrovelocity/actions/workflows/cml.yml) [![pre-commit.ci status](https://results.pre-commit.ci/badge/github/pinellolab/pyrovelocity/main.svg)](https://results.pre-commit.ci/latest/github/pinellolab/pyrovelocity/main) |
| Docs | [![Documentation Status](https://readthedocs.org/projects/pyrovelocity/badge/?version=latest)](https://pyrovelocity.readthedocs.io/en/latest/?badge=latest) [![Preprint](https://img.shields.io/badge/doi-10.1101/2022.09.12.507691v2-B31B1B)](https://doi.org/10.1101/2022.09.12.507691) |
| Package | [![PyPI - Version](https://img.shields.io/pypi/v/pyrovelocity.svg?logo=pypi&label=PyPI&logoColor=gold)](https://pypi.org/project/pyrovelocity/) [![PyPI - Python Version](https://img.shields.io/pypi/pyversions/pyrovelocity.svg?logo=python&label=Python&logoColor=gold)](https://pypi.org/project/pyrovelocity/) [![Docker iamge](https://img.shields.io/badge/docker-image-blue?logo=docker)](https://github.com/pinellolab/pyrovelocity/pkgs/container/pyrovelocity) |
| Meta | [![codecov](https://codecov.io/gh/pinellolab/pyrovelocity/branch/master/graph/badge.svg)](https://codecov.io/gh/pinellolab/pyrovelocity) [![code style - Black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black) [![License - MIT](https://img.shields.io/badge/license-AGPL%203-purple)](https://spdx.org/licenses/) |
| Meta | [![codecov](https://codecov.io/gh/pinellolab/pyrovelocity/branch/main/graph/badge.svg)](https://codecov.io/gh/pinellolab/pyrovelocity) [![code style - Black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black) [![License - MIT](https://img.shields.io/badge/license-AGPL%203-purple)](https://spdx.org/licenses/) |
"""

BIG_TITLE_STYLE = CSSStyle(
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2 changes: 1 addition & 1 deletion docs/conf.py
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Expand Up @@ -73,6 +73,6 @@
},
],
"source_repository": "https://github.com/pinellolab/pyrovelocity/",
"source_branch": "master",
"source_branch": "main",
"source_directory": "docs/",
}
2 changes: 1 addition & 1 deletion docs/contributing.md
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Expand Up @@ -51,7 +51,7 @@ If you are proposing a feature:

### Cloud

See the [reproducibility/environment](https://github.com/pinellolab/pyrovelocity/tree/master/reproducibility/environment) folder and associated README.md.
See the [reproducibility/environment](https://github.com/pinellolab/pyrovelocity/tree/main/reproducibility/environment) folder and associated README.md.

### Local

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4 changes: 2 additions & 2 deletions docs/installation.md
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Expand Up @@ -6,7 +6,7 @@

We currently only support linux amd64 with access to at least one GPU having NVIDIA drivers installed.
This is related to issues [such as this](https://github.com/google/jax/issues/7097) among the indirect dependencies.
We provide a [docker container](https://github.com/pinellolab/pyrovelocity/pkgs/container/pyrovelocity) for the same architecture. We also provide an [IaC development environment](https://github.com/pinellolab/pyrovelocity/blob/master/reproducibility/environment/README.md).
We provide a [docker container](https://github.com/pinellolab/pyrovelocity/pkgs/container/pyrovelocity) for the same architecture. We also provide an [IaC development environment](https://github.com/pinellolab/pyrovelocity/blob/main/reproducibility/environment/README.md).

If you are planning to attempt to install Pyro-Velocity on your own linux amd64 machine, it should be performed inside a virtual environment such as provided by [virtualenv](https://virtualenv.pypa.io/en/latest/) or [conda](https://github.com/conda-forge/miniforge#mambaforge).

Expand All @@ -25,7 +25,7 @@ The source for pyrovelocity can be downloaded from the [GitHub repository].
You can install the latest development version directly from github

```console
$ python -m pip install "pyrovelocity @ git+https://github.com/pinellolab/pyrovelocity.git@master"
$ python -m pip install "pyrovelocity @ git+https://github.com/pinellolab/pyrovelocity.git@main"
```

[github repository]: https://github.com/pinellolab/pyrovelocity
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2 changes: 1 addition & 1 deletion docs/source/notebooks/pyrovelocity_colab_template.ipynb
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Expand Up @@ -13,7 +13,7 @@
"cell_type": "markdown",
"metadata": {},
"source": [
"<a target=\"_blank\" href=\"https://colab.research.google.com/github/pinellolab/pyrovelocity/blob/master/docs/source/notebooks/pyrovelocity_colab_template.ipynb\">\n",
"<a target=\"_blank\" href=\"https://colab.research.google.com/github/pinellolab/pyrovelocity/blob/main/docs/source/notebooks/pyrovelocity_colab_template.ipynb\">\n",
" <img src=\"https://colab.research.google.com/assets/colab-badge.svg\" alt=\"Open In Colab\"/>\n",
"</a>"
]
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2 changes: 1 addition & 1 deletion justfile
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Expand Up @@ -26,7 +26,7 @@ container_work := container_home / "work"
git_username := env_var_or_default('GITHUB_USERNAME', 'pinellolab')
git_org_name := env_var_or_default('GITHUB_ORG_NAME', 'pinellolab')
git_repo_name := env_var_or_default('GITHUB_REPO_NAME', 'pyrovelocity')
git_branch_name := env_var_or_default('GITHUB_BRANCH_NAME', 'master')
git_branch_name := env_var_or_default('GITHUB_BRANCH_NAME', 'main')
container_registry := "ghcr.io/" + git_org_name + "/"
pod_accelerator_type := env_var_or_default('POD_ACCELERATOR_TYPE', 'nvidia-tesla-t4')
accelerator_node_selector := "gpu-type=" + pod_accelerator_type
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2 changes: 1 addition & 1 deletion reproducibility/environment/README.md
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Expand Up @@ -43,7 +43,7 @@ The expected workflow is to
GITHUB_USERNAME=username # github username associated to uploading startup scripts as github gists
GITHUB_ORG_NAME=githuborg # name of the github org or user containing the github repository with code for development
GITHUB_REPO_NAME=reponame # name of a github repository with a conda environment yaml file
GITHUB_BRANCH_NAME=master # name of github repository branch to checkout
GITHUB_BRANCH_NAME=main # name of github repository branch to checkout
GITHUB_REPO_CONDA_ENV_PATH_NAME=conda/environment-gpu.yml # path to conda environment yaml file in the github repository
GH_PAT=ghp_XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX # github personal access token with repo scope
GH_REPO=${GITHUB_USERNAME}/${GITHUB_REPO_NAME} # derived
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2 changes: 1 addition & 1 deletion scripts/git/update-filter-branches.sh
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Expand Up @@ -13,5 +13,5 @@ for branch in `git branch -a | grep remotes | grep -v HEAD | grep -E 'upstream/f
echo "Checking out ${branch#remotes/upstream/}"
git checkout ${branch#remotes/upstream/}
git reset --hard upstream/${branch#remotes/upstream/}
gt btr -p master
gt btr -p main
done

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