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tothpetroczylab
Picnic
Commits
a1806bd8
Commit
a1806bd8
authored
9 months ago
by
Maxim Scheremetjew
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release: Release preparation version 1.0.0-rc1.
parent
cc62e771
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1.0.0rc1
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1 merge request
!34
release: Release preparation version 1.0.0-rc1.
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README.md
+18
-5
18 additions, 5 deletions
README.md
requirements.txt
+1
-1
1 addition, 1 deletion
requirements.txt
setup.py
+2
-2
2 additions, 2 deletions
setup.py
with
21 additions
and
8 deletions
README.md
+
18
−
5
View file @
a1806bd8
...
...
@@ -24,7 +24,7 @@ A binary installer for the latest released version is available at the Python Pa
## Requirements
*
Python versions >=3.9,<3.1
2
*
Python versions >=3.9,<3.1
3
*
Download and unpack IUPred2A
*
Add IUPred2A to PYTHONPATH
*
Download and unpack STRIDE
...
...
@@ -61,12 +61,16 @@ $ export PYTHONPATH="$PWD"
## PICNIC is available on PyPI
PICNIC officially supports Python versions >=3.9,<3.1
2
.
PICNIC officially supports Python versions >=3.9,<3.1
3
.
```
shell
$
python3
--version
Python 3.11.5
$
python3
-m
pip
install
picnic_bio
$
python3
-m
venv picnic-env
$
source
picnic-env/bin/activate
$
(
picnic-env
)
% python
-m
pip
install
--upgrade
pip
$
(
picnic-env
)
% python
-m
pip
install
picnic_bio
```
## PICNIC is also installable from source
...
...
@@ -81,7 +85,8 @@ Once you have a copy of the source, you can embed it in your own Python package,
$
cd
picnic
$
python3
-m
venv picnic-env
$
source
picnic-env/bin/activate
(
picnic-env
)
$
python
-m
pip
install
.
$
(
picnic-env
)
% python
-m
pip
install
--upgrade
pip
$
(
picnic-env
)
$
python
-m
pip
install
.
```
## How to install PICNIC using Conda?
...
...
@@ -95,7 +100,11 @@ We have documented how to get around the catboost installation issue.
```
shell
$
conda config
--add
channels conda-forge
$
conda config
--set
channel_priority strict
$
conda create
-n
myenv
python
=[
3.9, 3.10, 3.11]
catboost
=
1.2.3
# Choose one of the supported Python versions, when creating the Conda environment: >=3.9,<3.13
# conda create -n myenv python=[3.9, 3.10, 3.11, 3.12] catboost
# e.g.
$
conda create
-n
myenv
python
=
3.11 catboost
$
conda activate myenv
(
myenv
)
$
python
-m
pip
install
picnic_bio
```
...
...
@@ -325,6 +334,10 @@ Finally, we need to upload these files to PyPi using Twine. Use the following co
directory. Enter the PyPi credentials to complete uploading the package.
```
shell
# Perform a test upload on testPyPI
(
packaging
)
$
twine upload
--repository
testpypi dist/
*
# Finally upload the distribution to PyPI
(
packaging
)
$
twine upload dist/
*
```
...
...
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requirements.txt
+
1
−
1
View file @
a1806bd8
# Project requirements
requests
~=2.31.0
catboost
=
=1.2.3
catboost
~
=1.2.3
matplotlib
~=3.7.2
pandas
~=2.2.1
Bio
~=1.5.2
...
...
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setup.py
+
2
−
2
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a1806bd8
...
...
@@ -9,7 +9,7 @@ with open("README.md", "r", encoding="utf-8") as fh:
setuptools
.
setup
(
name
=
"
picnic-bio
"
,
version
=
"
1.0.0-
beta3
"
,
version
=
"
1.0.0-
rc1
"
,
author
=
"
Anna Hadarovich <hadarovi@mpi-cbg.de>, Maxim Scheremetjew <schereme@mpi-cbg.de>
"
,
author_email
=
"
picnic@cd-code.org
"
,
description
=
"
PICNIC (Proteins Involved in CoNdensates In Cells) is a machine learning-based model that predicts proteins involved in biomolecular condensates.
"
,
...
...
@@ -43,7 +43,7 @@ setuptools.setup(
python_requires
=
"
>=3.9
"
,
install_requires
=
[
"
requests ~=2.31.0
"
,
"
catboost
=
=1.2.3
"
,
"
catboost
~
=1.2.3
"
,
"
matplotlib ~=3.7.2
"
,
"
pandas ~=2.2.1
"
,
"
Bio ~=1.5.2
"
,
...
...
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