From 2814f4c585abb2ed725443e6c588641b39a58e3b Mon Sep 17 00:00:00 2001 From: asistradition Date: Fri, 5 Feb 2021 11:51:56 -0500 Subject: [PATCH 1/8] Add vscode --- .gitignore | 3 +++ 1 file changed, 3 insertions(+) diff --git a/.gitignore b/.gitignore index 5355aa14..799b2917 100644 --- a/.gitignore +++ b/.gitignore @@ -70,3 +70,6 @@ target/ #Ipython Notebook .ipynb_checkpoints + +# VSCode +.vscode \ No newline at end of file From cc5959aa93ed73c9a75f6291e8e3b1584c1f3db0 Mon Sep 17 00:00:00 2001 From: asistradition Date: Wed, 7 Apr 2021 12:22:23 -0400 Subject: [PATCH 2/8] Add yeastract prior to repo --- data/yeast/YEASTRACT_20190713_BOTH.tsv | 1 + data/yeast/tf_names_yeastract.txt | 218 +++++++++++++++++++++++++ 2 files changed, 219 insertions(+) create mode 120000 data/yeast/YEASTRACT_20190713_BOTH.tsv create mode 100644 data/yeast/tf_names_yeastract.txt diff --git a/data/yeast/YEASTRACT_20190713_BOTH.tsv b/data/yeast/YEASTRACT_20190713_BOTH.tsv new file mode 120000 index 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--git a/inferelator/amusr_workflow.py b/inferelator/amusr_workflow.py index 5d914973..0dcbe14e 100644 --- a/inferelator/amusr_workflow.py +++ b/inferelator/amusr_workflow.py @@ -45,6 +45,8 @@ class MultitaskLearningWorkflow(single_cell_workflow.SingleCellWorkflow): def _num_obs(self): if self._task_objects is not None: return sum([t if t is not None else 0 for t in map(lambda x: x._num_obs, self._task_objects)]) + elif self._task_design is not None: + return sum([t.num_obs for t in self._task_design]) else: return None From 2c8350b00a8aa89f61441f79c58bcdcc0404bd5d Mon Sep 17 00:00:00 2001 From: asistradition Date: Thu, 29 Apr 2021 14:51:23 -0400 Subject: [PATCH 5/8] Restart workers after each amusr boostrap --- inferelator/distributed/dask_functions.py | 1 + 1 file changed, 1 insertion(+) diff --git a/inferelator/distributed/dask_functions.py b/inferelator/distributed/dask_functions.py index 55e4695d..e54d2567 100644 --- a/inferelator/distributed/dask_functions.py +++ b/inferelator/distributed/dask_functions.py @@ -81,6 +81,7 @@ def response_maker(y_df, i): DaskController.client.cancel(scatter_x) DaskController.client.cancel(scatter_priors) + DaskController.client.restart() return result_list From 512b151f0d7fe7d5fed8d0191001a12120a14bb7 Mon Sep 17 00:00:00 2001 From: asistradition Date: Thu, 6 May 2021 10:31:56 -0400 Subject: [PATCH 6/8] Add biorxiv link --- README.md | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index 7126e2e8..fce3f4b2 100644 --- a/README.md +++ b/README.md @@ -1,11 +1,12 @@ -# inferelator +# Inferelator 3.0 [![PyPI version](https://badge.fury.io/py/inferelator.svg)](https://badge.fury.io/py/inferelator) [![Travis](https://travis-ci.org/flatironinstitute/inferelator.svg?branch=release)](https://travis-ci.org/flatironinstitute/inferelator) [![codecov](https://codecov.io/gh/flatironinstitute/inferelator/branch/release/graph/badge.svg)](https://codecov.io/gh/flatironinstitute/inferelator) [![Documentation Status](https://readthedocs.org/projects/inferelator/badge/?version=latest)](https://inferelator.readthedocs.io/en/latest/?badge=latest) -The [inferelator](https://doi.org/10.1186/gb-2006-7-5-r36) is a package for gene regulatory network inference that is based on regularized regression. +The [Inferelator 3.0](https://www.biorxiv.org/content/10.1101/2021.05.03.442499v2) is a package for gene regulatory network inference that is based on regularized regression. +It is an update of the [Inferelator 2.0](https://ieeexplore.ieee.org/document/5334018), which is an update of the original [Inferelator](https://doi.org/10.1186/gb-2006-7-5-r36) It is maintained by the Bonneau lab in the [Systems Biology group of the Flatiron Institute](https://www.simonsfoundation.org/flatiron/center-for-computational-biology/systems-biology/). This repository is the actively developed inferelator package for python. It works for both single-cell and bulk transcriptome experiments. From 37acf510e34249a72a3bc2dfac8c2e0dd722faa7 Mon Sep 17 00:00:00 2001 From: asistradition Date: Thu, 6 May 2021 10:42:51 -0400 Subject: [PATCH 7/8] Add references to new paper --- docs/references.rst | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/docs/references.rst b/docs/references.rst index 5ab92466..d8020fb8 100644 --- a/docs/references.rst +++ b/docs/references.rst @@ -3,6 +3,8 @@ References * `R. Bonneau et al., “The Inferelator: an algorithm for learning parsimonious regulatory networks from systems-biology data sets de novo,” Genome Biology, vol. 7, p. R36, May 2006. `_ +* `A. Madar, A. Greenfield, H. Ostrer, E. Vanden-Eijnden, and R. Bonneau, “The inferelator 2.0: A scalable framework for reconstruction of dynamic regulatory network models,” in 2009 Annual International Conference of the IEEE Engineering in Medicine and Biology Society, Sep. 2009. `_ + * `A. Madar, A. Greenfield, E. Vanden-Eijnden, and R. Bonneau, “DREAM3: Network Inference Using Dynamic Context Likelihood of Relatedness and the Inferelator,” PLOS ONE, vol. 5, no. 3, p. e9803, Mar. 2010. `_ * `A. Greenfield, A. Madar, H. Ostrer, and R. Bonneau, “DREAM4: Combining Genetic and Dynamic Information to Identify Biological Networks and Dynamical Models,” PLOS ONE, vol. 5, no. 10, p. e13397, Oct. 2010. `_ @@ -21,5 +23,6 @@ References * `E. R. Miraldi et al., “Leveraging chromatin accessibility for transcriptional regulatory network inference in T Helper 17 Cells,” Genome Res., vol. 29, no. 3, pp. 449–463, Mar. 2019. `_ -* `C. A. Jackson, D. M. Castro, G.-A. Saldi, R. Bonneau, and D. Gresham, “Gene regulatory network reconstruction using single-cell RNA sequencing of barcoded genotypes in diverse environments,” bioRxiv, p. 581678, Apr. 2019. `_ +* `C. A. Jackson, D. M. Castro, G.-A. Saldi, R. Bonneau, and D. Gresham, “Gene regulatory network reconstruction using single-cell RNA sequencing of barcoded genotypes in diverse environments,” eLife, vol. 9, p. e51254, Jan. 2020. `_ +* `C. Skok Gibbs, C. A. Jackson, G.-A. Saldi et al. “Single-cell gene regulatory network inference at scale: The Inferelator 3.0,” bioRxiv, p. 2021.05.03.442499, May 2021. `_ From 7b959478156512785987e3f93cb1d5d44bfc5d97 Mon Sep 17 00:00:00 2001 From: CJACKSON <33259488+asistradition@users.noreply.github.com> Date: Wed, 30 Jun 2021 12:08:56 -0400 Subject: [PATCH 8/8] Create python-package.yml Change from travis to github actions --- .github/workflows/python-package.yml | 33 ++++++++++++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 .github/workflows/python-package.yml diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml new file mode 100644 index 00000000..0fad4479 --- /dev/null +++ b/.github/workflows/python-package.yml @@ -0,0 +1,33 @@ +# This workflow will install Python dependencies, run tests and lint with a variety of Python versions +# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions + +name: Inferelator CI + +on: [push, pull_request] + +jobs: + build: + + runs-on: ubuntu-latest + strategy: + fail-fast: false + matrix: + python-version: [3.7, 3.8, 3.9] + + steps: + - uses: actions/checkout@v2 + - name: Set up Python ${{ matrix.python-version }} + uses: actions/setup-python@v2 + with: + python-version: ${{ matrix.python-version }} + - name: Install dependencies + run: | + python -m pip install --upgrade pip + python -m pip install -r requirements.txt + python -m pip install -r requirements-test.txt + python -m pip install -r requirements-multiprocessing.txt + - name: Test with pytest & coverage + run: | + python -m coverage run -m pytest + - name: Upload Coverage to Codecov + uses: codecov/codecov-action@v1