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