Merge pull request #39 from saezlab/dev

LIANA+ merge

.github/workflows/main.yml

@@ -1,6 +1,3 @@
-# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
-# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python
-
 name: Python package
 
 on:
@@ -15,28 +12,29 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.7", "3.9"]
+        python-version: ["3.8", "3.10"]
 
     steps:
     - uses: actions/checkout@v3
     - name: Set up Python ${{ matrix.python-version }}
       uses: actions/setup-python@v3
       with:
         python-version: ${{ matrix.python-version }}
+    - name: Install Poetry
+      run: |
+        curl -sSL https://install.python-poetry.org | python -
     - name: Install dependencies
       run: |
-        python -m pip install --upgrade pip
-        python -m pip install flake8 pytest pytest-cov git+https://github.com/saezlab/omnipath adjustText numpydoc setuptools
-        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+        poetry install --extras "full"
     - name: Lint with flake8
       run: |
         # stop the build if there are Python syntax errors or undefined names
-        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+        poetry run flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
         # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
-        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+        poetry run flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
     - name: Test and add coverage
       run: |
-        pytest --cov --disable-warnings liana
+        poetry run pytest --cov --disable-warnings liana
     - name: Upload coverage reports to Codecov
       run: |
         curl -Os https://uploader.codecov.io/latest/linux/codecov
@@ -53,18 +51,19 @@ jobs:
       uses: actions/setup-python@v2
       with:
         python-version: 3.9
-    - name: Install dependencies
+    - name: Install Poetry
       run: |
         python -m pip install --upgrade pip
-        python -m pip install flake8 pytest pytest-cov git+https://github.com/saezlab/omnipath adjustText IPython
-        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+        python -m pip install poetry
+    - name: Install dependencies
+      run: |
+        poetry install --extras "full"
     - name: Lint with flake8
       run: |
         # stop the build if there are Python syntax errors or undefined names
-        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+        poetry run flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
         # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
-        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+        poetry run flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
     - name: Test
       run: |
-        pytest --disable-warnings .
-
+        poetry run pytest --disable-warnings .

README.md

@@ -1,4 +1,4 @@
-# LIANA: a LIgand-receptor ANalysis frAmework <img src="https://github.com/saezlab/liana-py/blob/main/docs/source/logo.png?raw=true" align="right" height="125">
+# LIANA+: a one-stop-shop framework for cell-cell communication <img src="https://raw.githubusercontent.com/saezlab/liana-py/dev/docs/source/_static/logo.png?raw=true" align="right" height="125">
 
 <!-- badges: start -->
 [![main](https://github.com/saezlab/liana-py/actions/workflows/main.yml/badge.svg)](https://github.com/saezlab/liana-py/actions)
@@ -8,87 +8,58 @@
 [![Downloads](https://pepy.tech/badge/liana)](https://pepy.tech/project/liana)
 <!-- badges: end -->
 
-LIANA is a Ligand-Receptor inference framework that enables the use of any LR method with any resource.
-This is its faster and memory efficient Python implementation, an R version is also available [here](https://github.com/saezlab/liana).
+LIANA+ is an efficient framework that integrates and extends existing methods and knowledge to study cell-cell communication in single-cell, spatially-resolved, and multi-modal omics data. 
 
+<img src="https://raw.githubusercontent.com/saezlab/liana-py/dev/docs/source/_static/abstract.png?raw=true" width="700" align="center">
 
-## Tutorials & Documentation
 
-- [LIANA's basic tutorial](https://liana-py.readthedocs.io/en/latest/notebooks/basic_usage.html) in dissociated single-cell data
+## Contributions & Development
 
-- [LIANA with MOFA](https://liana-py.readthedocs.io/en/latest/notebooks/mofatalk.html). Using MOFA to infer intercellular communication programmes across samples and conditions, as initially proposed by cell2cell-Tensor
+LIANA+ is currently at it's alpha stage - i.e. we are actively working on improving it.
 
-- [Multicellular programmes with MOFA](https://liana-py.readthedocs.io/en/latest/notebooks/mofacellular.html). Using MOFA to obtain coordinates
-gene expression programmes across samples and conditions, as done in [Ramirez et al., 2023](https://europepmc.org/article/ppr/ppr620471)
+The API visible to the user should be stable, specifically `liana.method.sc`, but some differences in terms of secondary parameters, or default settings are possible.
 
-- [LIANA with cell2cell-Tensor](https://liana-py.readthedocs.io/en/latest/notebooks/liana_c2c.html) to extract intercellular communication programmes across samples and conditions. Extensive tutorials combining LIANA & [cell2cell-Tensor](https://www.nature.com/articles/s41467-022-31369-2) are available [here](https://ccc-protocols.readthedocs.io/en/latest/index.html).
+More importantly, we welcome suggestions, ideas, and contributions! Please use do not hesitate to contact us, or use the issues or the [LIANA+ Development project](https://github.com/orgs/saezlab/projects/16) to make suggestions.
 
-- We also refer users to the [Cell-cell communication chapter](https://www.sc-best-practices.org/mechanisms/cell_cell_communication.html) in the [best-practices guide from Theis lab](https://www.nature.com/articles/s41576-023-00586-w). There we provide an overview of the common limitations and assumptions in CCC inference from (dissociated single-cell) transcriptomics data.
 
-For further information please check LIANA's [API documentation](https://liana-py.readthedocs.io/en/latest/api.html).
+## Tutorials
+
+### Single-cell/Dissociated Data
+
+- [LIANA's basic tutorial](https://liana-py.readthedocs.io/en/latest/notebooks/basic_usage.html) in dissociated single-cell data
 
-## Install LIANA
+### Spatial Data
 
-Install liana's stable version:
-```
-pip install liana
-```
+- [Learn spatially-informed relationships  with MISTy](https://liana-py.readthedocs.io/en/latest/notebooks/misty.html) across (multi-)views
 
-Install liana's most up-to-date version:
-```
-pip install git+https://github.com/saezlab/liana-py
-```
+- Estimate local spatially-informed bivariate metrics with [LIANA's bivariate scores](https://liana-py.readthedocs.io/en/latest/notebooks/bivariate.html)
 
-## Methods
+### Multi-condition
 
-The methods implemented in this repository are:
+- [Hypothesis-testing for CCC with PyDeSeq2](https://liana-py.readthedocs.io/en/latest/notebooks/targeted.html) that also shows the inference of causal **intracellular** signalling networks
 
-- [CellPhoneDBv2](https://github.com/Teichlab/cellphonedb)
-- [NATMI](https://github.com/forrest-lab/NATMI)
-- [Connectome](https://github.com/msraredon/Connectome)
-- [SingleCellSignalR](https://github.com/SCA-IRCM/SingleCellSignalR)
-- [CellChat](https://github.com/sqjin/CellChat) (+)
-- *1-vs-rest* expression `LogFC` score
-- `Geometric Mean` - ligand-receptor geometric mean with pvalues obtained 
-via the permutation approach implemented by CellPhoneDBv2
-- `rank_aggregate` of the predictions calculated with the
-[RobustRankAggregate](https://academic.oup.com/bioinformatics/article/28/4/573/213339) method
+- [Multicellular programmes with MOFA](https://liana-py.readthedocs.io/en/latest/notebooks/mofacellular.html). Using MOFA to obtain coordinates
+gene expression programmes across samples and conditions, as done in [Ramirez et al., 2023](https://europepmc.org/article/ppr/ppr620471)
+
+- [LIANA with MOFA](https://liana-py.readthedocs.io/en/latest/notebooks/mofatalk.html). Using MOFA to infer intercellular communication programmes across samples and conditions, as initially proposed by cell2cell-Tensor
+
+- [LIANA with cell2cell-Tensor](https://liana-py.readthedocs.io/en/latest/notebooks/liana_c2c.html) to extract intercellular communication programmes across samples and conditions. Extensive tutorials combining LIANA & [cell2cell-Tensor](https://www.nature.com/articles/s41467-022-31369-2) are available [here](https://ccc-protocols.readthedocs.io/en/latest/index.html).
 
-(+) A resource-independent adaptation of the CellChat LR inference functions.
 
-## Ligand-Receptor Resources
+### Others
 
-The following CCC resources are accessible via this pipeline:
+- We also refer users to the [Cell-cell communication chapter](https://www.sc-best-practices.org/mechanisms/cell_cell_communication.html) in the [best-practices guide from Theis lab](https://www.nature.com/articles/s41576-023-00586-w). There we provide an overview of the common limitations and assumptions in CCC inference from (dissociated single-cell) transcriptomics data.
 
-- Consensus ($)
-- CellCall
-- CellChatDB
-- CellPhoneDB
-- Ramilowski2015
-- Baccin2019
-- LRdb
-- Kiroauc2010
-- ICELLNET
-- iTALK
-- EMBRACE
-- HPMR
-- Guide2Pharma
-- ConnectomeDB2020
-- CellTalkDB
-- MouseConsensus (#)
 
-($) LIANA's default `Consensus` resource was generated from several expert-curated resources, 
-filtered to additional quality control steps including literature support, complex re-union/consensus,
-and localisation.
+## API
+For further information please check LIANA's [API documentation](https://liana-py.readthedocs.io/en/latest/api.html).
 
-(#) Consensus Resource converted to murine homologs.
 
 
-## Cite LIANA:
+## Cite LIANA+:
 
-Dimitrov, D., Türei, D., Garrido-Rodriguez M., Burmedi P.L., Nagai, J.S., Boys, C., Flores, R.O.R., Kim, H., Szalai, B., Costa, I.G., Valdeolivas, A., Dugourd, A. and Saez-Rodriguez, J. Comparison of methods and resources for cell-cell communication inference from single-cell RNA-Seq data. Nat Commun 13, 3224 (2022). https://doi.org/10.1038/s41467-022-30755-0
-Also, if you use the OmniPath CCC Resource for your analysis, please cite:
+Dimitrov, D. ... Saez-Rodriguez, J.
 
-Türei, D., Valdeolivas, A., Gul, L., Palacio‐Escat, N., Klein, M., Ivanova, O., Ölbei, M., Gábor, A., Theis, F., Módos, D. and Korcsmáros, T., 2021. Integrated intra‐and intercellular signaling knowledge for multicellular omics analysis. Molecular systems biology, 17(3), p.e9923. https://doi.org/10.15252/msb.20209923
+Dimitrov, D., Türei, D., Garrido-Rodriguez M., Burmedi P.L., Nagai, J.S., Boys, C., Flores, R.O.R., Kim, H., Szalai, B., Costa, I.G., Valdeolivas, A., Dugourd, A. and Saez-Rodriguez, J. Comparison of methods and resources for cell-cell communication inference from single-cell RNA-Seq data. Nat Commun 13, 3224 (2022). https://doi.org/10.1038/s41467-022-30755-0
 
 Similarly, please consider citing any of the methods and/or resources implemented in liana, that were particularly relevant for your research!