brie 2.2.2__tar.gz → 2.2.3__tar.gz

{brie-2.2.2 → brie-2.2.3}/.gitignore

@@ -1,6 +1,7 @@
 .DS_Store*
 .vscode/
 temp/
+doc/*.ipynb
 
 # Byte-compiled / optimized / DLL files
 __pycache__/

{brie-2.2.2 → brie-2.2.3}/PKG-INFO

@@ -1,16 +1,30 @@
 Metadata-Version: 2.1
 Name: brie
-Version: 2.2.2
+Version: 2.2.3
 Summary: BRIE: Bayesian regression for isoform estimate
 Home-page: https://brie.readthedocs.io
 Author: Yuanhua Huang
 Author-email: yuanhua@hku.hk
 License: Apache-2.0
 Keywords: RNA splicing,Bayesian regression,single cell RNA-seq,variantional inference
-Platform: UNKNOWN
 Requires-Python: >=3.5
-Provides-Extra: docs
 License-File: LICENSE
+Requires-Dist: anndata>=0.6
+Requires-Dist: scanpy>=1.5
+Requires-Dist: pysam>=0.15.2
+Requires-Dist: numpy>=1.18.0
+Requires-Dist: scipy>=1.4.1
+Requires-Dist: statsmodels>=0.11
+Requires-Dist: pandas>=0.23.0
+Requires-Dist: h5py>=2.9.0
+Requires-Dist: matplotlib>=3.1.2
+Requires-Dist: seaborn>=0.10.0
+Requires-Dist: tensorflow>=2.0.0
+Requires-Dist: tensorflow-probability>=0.8.0
+Requires-Dist: scikit-learn>=0.23
+Requires-Dist: click>=7.0.0
+Provides-Extra: docs
+Requires-Dist: sphinx_bootstrap_theme; extra == "docs"
 
 |PyPI| |Docs| |Build Status|
 
@@ -125,5 +139,3 @@ References
   quantification in single cells 
   <https://genomebiology.biomedcentral.com/articles/10.1186/s13059-017-1248-5>`_. 
   \ **Genome Biology**\, 2017; 18(1):123.
-
-

{brie-2.2.2 → brie-2.2.3}/brie/plot/LRtest_plot.py

@@ -75,7 +75,7 @@ def volcano(adata, x="cell_coeff", y="ELBO_gain", index=0, score_red=4,
     plt.scatter(xval[~idx], yval[~idx], color="gray")
     plt.scatter(xval[idx], yval[idx], color="firebrick")
     
-    lable = adata.var.index if anno_id is 'index' else adata.var[anno_id]
+    lable = adata.var.index if anno_id == 'index' else adata.var[anno_id]
     
     texts = []
     for i in idx_anno:

{brie-2.2.2 → brie-2.2.3}/brie/plot/base_plot.py

@@ -35,7 +35,7 @@ def counts(adata, genes, size='Psi', color=None, gene_key='index',
     if ncol is None:
         ncol = min(4, len(genes))
     if nrow is None:
-        nrow = np.ceil(len(genes) / ncol)
+        nrow = int(np.ceil(len(genes) / ncol))
     
     if color is None:
         color_use = None

brie-2.2.3/brie/version.py

@@ -0,0 +1,2 @@
+__version__ = "2.2.3"
+

{brie-2.2.2 → brie-2.2.3}/brie.egg-info/PKG-INFO

@@ -1,16 +1,30 @@
 Metadata-Version: 2.1
 Name: brie
-Version: 2.2.2
+Version: 2.2.3
 Summary: BRIE: Bayesian regression for isoform estimate
 Home-page: https://brie.readthedocs.io
 Author: Yuanhua Huang
 Author-email: yuanhua@hku.hk
 License: Apache-2.0
 Keywords: RNA splicing,Bayesian regression,single cell RNA-seq,variantional inference
-Platform: UNKNOWN
 Requires-Python: >=3.5
-Provides-Extra: docs
 License-File: LICENSE
+Requires-Dist: anndata>=0.6
+Requires-Dist: scanpy>=1.5
+Requires-Dist: pysam>=0.15.2
+Requires-Dist: numpy>=1.18.0
+Requires-Dist: scipy>=1.4.1
+Requires-Dist: statsmodels>=0.11
+Requires-Dist: pandas>=0.23.0
+Requires-Dist: h5py>=2.9.0
+Requires-Dist: matplotlib>=3.1.2
+Requires-Dist: seaborn>=0.10.0
+Requires-Dist: tensorflow>=2.0.0
+Requires-Dist: tensorflow-probability>=0.8.0
+Requires-Dist: scikit-learn>=0.23
+Requires-Dist: click>=7.0.0
+Provides-Extra: docs
+Requires-Dist: sphinx_bootstrap_theme; extra == "docs"
 
 |PyPI| |Docs| |Build Status|
 
@@ -125,5 +139,3 @@ References
   quantification in single cells 
   <https://genomebiology.biomedcentral.com/articles/10.1186/s13059-017-1248-5>`_. 
   \ **Genome Biology**\, 2017; 18(1):123.
-
-

{brie-2.2.2 → brie-2.2.3}/brie.egg-info/entry_points.txt

@@ -4,4 +4,3 @@ brie-count = brie.bin.count:main
 brie-quant = brie.bin.quant:main
 brie1 = brie.version1.brie:main
 brie1-diff = brie.version1.brie_diff:main
-

{brie-2.2.2 → brie-2.2.3}/doc/brie_quant.rst

@@ -46,6 +46,8 @@ Example command line for mode 2:
 
 .. code-block:: bash
 
+  # keep the following line if you have GPU and want to specify a card
+  CUDA_VISIBLE_DEVICES=1 \
   brie-quant -i out_dir/brie_count.h5ad -o out_dir/brie_quant_aggr.h5ad --interceptMode gene
   
   
@@ -177,10 +179,10 @@ you are using):
       -g GENE_FILE, --geneFile=GENE_FILE
                             File for gene features in tsv[.gz] with gene and feature ids.
       -o OUT_FILE, --out_file=OUT_FILE
-                            Full path of output file for annData in h5ad [default:
-                            $inFile/brie_quant.h5ad]
-      --LRTindex=LRT_INDEX  Index (0-based) of cell features to test with LRT: All, None
-                            or comma separated integers [default: None]
+                            Full path of output file for annData in h5ad
+                            [default: $inFile/brie_quant.h5ad]
+      --LRTindex=LRT_INDEX  Index (0-based) of cell features to test with LRT: 
+                            All, None or comma separated integers [default: None]
       --testBase=TEST_BASE  Features in testing base model: full, null  [default: full]
       --interceptMode=INTERCEPT_MODE
                             Intercept mode: gene, cell or None [default: None]
@@ -194,8 +196,8 @@ you are using):
                             Minimum unique counts for fitltering genes [default: 10]
         --minCell=MIN_CELL  Minimum number of cells with unique count for fitltering genes
                             [default: 30]
-        --minMIF=MIN_MIF    Minimum minor isoform frequency in unique count [default:
-                            0.001]
+        --minMIF=MIN_MIF    Minimum minor isoform frequency in unique count 
+                            [default: 0.001]
 
       VI Optimization:
         --MCsize=MC_SIZE    Sample size for Monte Carlo Expectation [default: 3]
@@ -205,3 +207,5 @@ you are using):
                             Element size per batch: n_gene * total cell [default: 500000]
         --pseudoCount=PSEUDO_COUNT
                             Pseudo count to add on unique count matrices [default: 0.01]
+        -p NPROC, --nproc=NPROC
+                            Number of processes for computing [default: 6]

{brie-2.2.2 → brie-2.2.3}/doc/install.rst

@@ -9,11 +9,12 @@ easier and cleaner management of dependent packages, particularly TensorFlow and
 TensorFlow-probability, which are under active development.
 
 The following command line in terminal (Linux or MacOS) will create a conda 
-environment with name ``TFProb``, probably in the path ``~/.conda/envs/TFProb``:
+environment with name ``TFProb``, probably in the path ``~/.conda/envs/TFProb``
+(tested on Python 3.7 to 3.11):
 
 .. code-block:: bash
   
-  conda create -n TFProb python=3.7
+  conda create -n TFProb python=3.11
 
 Alternatively, you can create the environment in another path by replacing 
 ``-n TFProb`` with ``-p ANY_PATH/TFProb`` to specify the path for conda 
@@ -51,32 +52,29 @@ your own conda environment.
 GPU usage
 =========
 One of the key benefits of using TensorFlow backend is its direct support of 
-GPU for substantial speedups (generally >10x). Here is one way to set up GPU 
-configurations with NVIDIA GPU on Ubuntu:
+GPU for substantial speedups (generally >10x). In general, the above 
+installation should directly support GPU use as default by using the newest 
+tensorflow and tensorflow-probability. 
 
-.. code-block:: bash
+To check if the installation is compatible with GPUs, you can print out the 
+detectable GPU cards, as below (it gives `[ ]` if failing to setup properly):
 
-  pip install -U tensorflow-gpu
-  conda install -c anaconda cudatoolkit
+.. code-block:: html
 
-Make sure that you have compatible versions between tensorflow and NVIDIA CUDA. 
-You can check TF's test `here <https://www.tensorflow.org/install/source#gpu>`_.
-For more information on GPU configuration, please refer to the 
-`Tensorflow documentation`_ or `anaconda GPU`_.
+  $ python3 -c "import tensorflow as tf; print(tf.config.list_physical_devices('GPU'))"
+    [PhysicalDevice(name='/physical_device:GPU:0', device_type='GPU'), ...]
 
-.. _Tensorflow documentation: https://www.tensorflow.org/guide/gpu
-.. _anaconda GPU: https://docs.anaconda.com/anaconda/user-guide/tasks/gpu-packages/
+However, occasionally, the newest TensorFlow may not be stable or compatible
+widely, for example the `tensorflow[and-cuda]==2.16.1` is not compatible with GPUs,
+see discussion `here <https://github.com/tensorflow/tensorflow/issues/63362#issuecomment-2053849484>`_.
 
-Once successfully configured, you will see log info like the following when 
-using ``brie-quant``:
+Here is one way to use a lower version for GPU configurations with NVIDIA GPU 
+on Ubuntu (tested on 21/04/2024):
 
-.. code-block:: html
-
-  $ brie-quant
-    I tensorflow/stream_executor/platform/default/dso_loader.cc:53] 
-    Successfully opened dynamic library libcudart.so.11.0
-    Welcome to brie-quant in BRIE v2.0.5!
+.. code-block:: bash
 
+  pip install tensorflow-probability==0.23.0
+  pip install tensorflow[and-cuda]==2.15.1
 
 .. note::
    At the moment, TensorFlow calls all available GPUs, which is not necessary. 

{brie-2.2.2 → brie-2.2.3}/doc/release.rst

@@ -5,6 +5,11 @@ Release notes
 Release in future
 =================
 
+Release v2.2.3 (15/05/2022)
+===========================
+* minor fix in plotting function brie.pl.count()
+* add submodule brie-tutorials
+
 Release v2.2.2 (04/11/2022)
 ===========================
 * support limit the CPU threads used by tensorflow in brie-quant (default 6)

brie-2.2.2/brie/version.py

@@ -1,2 +0,0 @@
-__version__ = "2.2.2"
-