From e64b8ed00042de0c6a9de84cfa7e4223bdcf799a Mon Sep 17 00:00:00 2001 From: bastien-mva <bastien.batardiere@gmail.com> Date: Mon, 23 Oct 2023 23:01:30 +0200 Subject: [PATCH 1/8] changed image in publishing package and build package. --- .gitlab-ci.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml index e45adf60..671bb811 100644 --- a/.gitlab-ci.yml +++ b/.gitlab-ci.yml @@ -32,7 +32,7 @@ tests: build_package: stage: build - image: "registry.forgemia.inra.fr/jbleger/docker-image-pandas-torch-sphinx:master" + image: "registry.forgemia.inra.fr/bbatardiere/docker-image-pandas-torch-sphinx-jupyter" before_script: - pip install build script: @@ -59,7 +59,7 @@ publish_package: pages: stage: publish - image: "registry.forgemia.inra.fr/jbleger/docker-image-pandas-torch-sphinx:master" + image: "registry.forgemia.inra.fr/bbatardiere/docker-image-pandas-torch-sphinx-jupyter" before_script: - pip install '.[build-doc]' script: -- GitLab From a30e85504eda782800d5d25bc45fb8a837dc61cc Mon Sep 17 00:00:00 2001 From: bastien-mva <bastien.batardiere@gmail.com> Date: Mon, 23 Oct 2023 23:05:36 +0200 Subject: [PATCH 2/8] add the ZIPln in the readme. --- README.md | 12 +++++++++--- 1 file changed, 9 insertions(+), 3 deletions(-) diff --git a/README.md b/README.md index f8adaa3f..71d47bbc 100644 --- a/README.md +++ b/README.md @@ -24,7 +24,7 @@ The getting started can be found [here](https://forgemia.inra.fr/bbatardiere/pyp The package comes with an ecological data set to present the functionality ``` import pyPLNmodels -from pyPLNmodels.models import PlnPCAcollection, Pln +from pyPLNmodels.models import PlnPCAcollection, Pln, ZIPln from pyPLNmodels.oaks import load_oaks oaks = load_oaks() ``` @@ -45,9 +45,15 @@ transformed_data = pln.transform() pca = PlnPCAcollection.from_formula("counts ~ 1 + tree + dist2ground + orientation ", data = oaks, take_log_offsets = True, ranks = [3,4,5]) pca.fit() print(pca) -transformed_data = pln.transform() +transformed_data = pca.transform() +``` +### Zero inflated Poisson Log normal Model (aka ZIPln) +``` +zi = ZIPln.from_formula("counts ~ 1 + tree + dist2ground + orientation ", data = oaks, take_log_offsets = True, ranks = [3,4,5]) +zi.fit() +zi(pca) +transformed_data = zi.transform() ``` - ## 🛠Installation -- GitLab From ac35834b9095083db7b956fcdc89e10c41933166 Mon Sep 17 00:00:00 2001 From: bastien-mva <bastien.batardiere@gmail.com> Date: Mon, 23 Oct 2023 23:08:56 +0200 Subject: [PATCH 3/8] not enough ===== under the ZIPLN --- docs/source/zipln.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/source/zipln.rst b/docs/source/zipln.rst index ae0e1e81..ccd9573c 100644 --- a/docs/source/zipln.rst +++ b/docs/source/zipln.rst @@ -1,6 +1,6 @@ ZIPln -=== +===== .. autoclass:: pyPLNmodels.ZIPln :members: -- GitLab From a9cdcc2b8066c897c07b0e8ff05f470bca990239 Mon Sep 17 00:00:00 2001 From: bastien-mva <bastien.batardiere@gmail.com> Date: Mon, 23 Oct 2023 23:12:52 +0200 Subject: [PATCH 4/8] minor change --- docs/source/zipln.rst | 1 - 1 file changed, 1 deletion(-) diff --git a/docs/source/zipln.rst b/docs/source/zipln.rst index ccd9573c..17fbac45 100644 --- a/docs/source/zipln.rst +++ b/docs/source/zipln.rst @@ -1,4 +1,3 @@ - ZIPln ===== -- GitLab From 29ad9fdbd83598beac3600e02965421364e69026 Mon Sep 17 00:00:00 2001 From: bastien-mva <bastien.batardiere@gmail.com> Date: Mon, 23 Oct 2023 23:48:21 +0200 Subject: [PATCH 5/8] typo in th eREADME --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 71d47bbc..ad011628 100644 --- a/README.md +++ b/README.md @@ -45,7 +45,7 @@ transformed_data = pln.transform() pca = PlnPCAcollection.from_formula("counts ~ 1 + tree + dist2ground + orientation ", data = oaks, take_log_offsets = True, ranks = [3,4,5]) pca.fit() print(pca) -transformed_data = pca.transform() +transformed_data = pca.best_model().transform() ``` ### Zero inflated Poisson Log normal Model (aka ZIPln) ``` -- GitLab From 534dd46a8edf80439c53a0c72738a6ce4d885fb9 Mon Sep 17 00:00:00 2001 From: bastien-mva <bastien.batardiere@gmail.com> Date: Tue, 24 Oct 2023 00:01:20 +0200 Subject: [PATCH 6/8] useless seaborn --- pyPLNmodels/_initialization.py | 1 - 1 file changed, 1 deletion(-) diff --git a/pyPLNmodels/_initialization.py b/pyPLNmodels/_initialization.py index fe649fe0..95b71246 100644 --- a/pyPLNmodels/_initialization.py +++ b/pyPLNmodels/_initialization.py @@ -4,7 +4,6 @@ from typing import Optional from ._utils import _log_stirling import time from sklearn.decomposition import PCA -import seaborn as sns import matplotlib.pyplot as plt import numpy as np -- GitLab From fb216d30fb2bce4d635108496de5efb2dbabdc1e Mon Sep 17 00:00:00 2001 From: bastien-mva <bastien.batardiere@gmail.com> Date: Tue, 24 Oct 2023 00:08:52 +0200 Subject: [PATCH 7/8] typo in the README --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index ad011628..25afa02b 100644 --- a/README.md +++ b/README.md @@ -51,7 +51,7 @@ transformed_data = pca.best_model().transform() ``` zi = ZIPln.from_formula("counts ~ 1 + tree + dist2ground + orientation ", data = oaks, take_log_offsets = True, ranks = [3,4,5]) zi.fit() -zi(pca) +print(zi) transformed_data = zi.transform() ``` -- GitLab From 483772af70f2735481bc77d84629d56877be7b9b Mon Sep 17 00:00:00 2001 From: bastien-mva <bastien.batardiere@gmail.com> Date: Tue, 24 Oct 2023 00:11:36 +0200 Subject: [PATCH 8/8] another typo. --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 25afa02b..267975de 100644 --- a/README.md +++ b/README.md @@ -49,7 +49,7 @@ transformed_data = pca.best_model().transform() ``` ### Zero inflated Poisson Log normal Model (aka ZIPln) ``` -zi = ZIPln.from_formula("counts ~ 1 + tree + dist2ground + orientation ", data = oaks, take_log_offsets = True, ranks = [3,4,5]) +zi = ZIPln.from_formula("counts ~ 1 + tree + dist2ground + orientation ", data = oaks, take_log_offsets = True) zi.fit() print(zi) transformed_data = zi.transform() -- GitLab