From 6b5c354a41b18f03e82348280a4397116d9eb794 Mon Sep 17 00:00:00 2001 From: jonasscheid Date: Sat, 9 Dec 2023 12:49:32 +0000 Subject: [PATCH 1/7] prepare release 3.3.2 --- CHANGELOG.md | 13 +++++++++++++ README.md | 2 +- epytope/tutorials/EpitopePrediction.ipynb | 19 +++++++++++-------- setup.py | 6 +++--- 4 files changed, 28 insertions(+), 12 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 29cf4cc..c8996d7 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,6 +3,19 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). +## v3.3.2 - 2023-12-15 + +### `Added` + +- [#93](https://github.com/KohlbacherLab/epytope/pull/93) Added NetMHCIIpan version 4.2 interface [#92](https://github.com/KohlbacherLab/epytope/issues/92) +- [#96](https://github.com/KohlbacherLab/epytope/pull/93) Added NetMHCIIpan version 4.3 interface [#95](https://github.com/KohlbacherLab/epytope/issues/95) + +### `Changed` + +### `Fixed` + +- [#93](https://github.com/KohlbacherLab/epytope/pull/93) Fixed length restriction of NetMHCIIpan interfaces [#91](https://github.com/KohlbacherLab/epytope/issues/91) + ## v3.3.1 - 2023-04-25 ### `Added` diff --git a/README.md b/README.md index 8db4611..284a987 100644 --- a/README.md +++ b/README.md @@ -63,7 +63,7 @@ Currently **epytope** provides implementations of several prediction methods or - [NetMHC](https://pubmed.ncbi.nlm.nih.gov/26515819/) 3.0, 3.4, 4.0 - [NetMHCII](https://pubmed.ncbi.nlm.nih.gov/29315598/) 2.2, 2.3 - [NetMHCpan](https://pubmed.ncbi.nlm.nih.gov/28978689/) 2.4, 2.8, 3.0, 4.0, 4.1 - - [NetMHCIIpan](https://pubmed.ncbi.nlm.nih.gov/32406916/) 3.0, 3.1, 4.0, 4.1 + - [NetMHCIIpan](https://pubmed.ncbi.nlm.nih.gov/32406916/) 3.0, 3.1, 4.0, 4.1, 4.2, 4.3 - [PickPocket](https://pubmed.ncbi.nlm.nih.gov/19297351/) 1.1 - [NetCTLpan](https://pubmed.ncbi.nlm.nih.gov/20379710/) 1.1 - Epitope Selection diff --git a/epytope/tutorials/EpitopePrediction.ipynb b/epytope/tutorials/EpitopePrediction.ipynb index fb174c8..92694a7 100644 --- a/epytope/tutorials/EpitopePrediction.ipynb +++ b/epytope/tutorials/EpitopePrediction.ipynb @@ -28,14 +28,17 @@ }, { "cell_type": "code", - "execution_count": 1, + "execution_count": null, "metadata": {}, "outputs": [ { - "name": "stderr", - "output_type": "stream", - "text": [ - "Using TensorFlow backend.\n" + "ename": "", + "evalue": "", + "output_type": "error", + "traceback": [ + "\u001b[1;31mRunning cells with 'epytope' requires the ipykernel package.\n", + "\u001b[1;31mRun the following command to install 'ipykernel' into the Python environment. \n", + "\u001b[1;31mCommand: 'conda install -n epytope ipykernel --update-deps --force-reinstall'" ] } ], @@ -202,10 +205,10 @@ "output_type": "stream", "text": [ "netmhc 3.0a,3.4,4.0\n", - "netmhcpan 2.4,2.8,3.0,4.0\n", + "netmhcpan 2.4,2.8,3.0,4.0,4.1\n", "netmhcstabpan 1.0\n", "netmhcii 2.2\n", - "netmhciipan 3.0,3.1\n", + "netmhciipan 3.0,3.1,4.0,4.1,4.2,4.3\n", "pickpocket 1.1\n", "netctlpan 1.1\n", "syfpeithi 1.0\n", @@ -1085,7 +1088,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.6.13" + "version": "3.7.12" } }, "nbformat": 4, diff --git a/setup.py b/setup.py index c432465..08c327a 100644 --- a/setup.py +++ b/setup.py @@ -21,7 +21,7 @@ name='epytope', # Version: - version='3.3.1', + version='3.3.2', description='A Framework for Epitope Detection and Vaccine Design', long_description=long_description, @@ -35,8 +35,8 @@ author_email='benjamin.schubert@helmholtz-muenchen.de, walzer@ebi.ac.uk, christopher.mohr@uni-tuebingen.de, leon.kuchenbecker@uni-tuebingen.de ', # maintainer details - maintainer='Christopher Mohr', - maintainer_email='christopher.mohr@uni-tuebingen.de', + maintainer='Christopher Mohr, Jonas Scheid', + maintainer_email='contact.cmohr@gmail.com, jonas.scheid@uni-tuebingen.de', # Choose your license license='BSD', From 94c37b2f4981bcff5e214971da74d4fe732fcc8f Mon Sep 17 00:00:00 2001 From: jonasscheid Date: Sat, 9 Dec 2023 12:55:48 +0000 Subject: [PATCH 2/7] clean epp tutorial --- epytope/tutorials/EpitopePrediction.ipynb | 13 +++++-------- 1 file changed, 5 insertions(+), 8 deletions(-) diff --git a/epytope/tutorials/EpitopePrediction.ipynb b/epytope/tutorials/EpitopePrediction.ipynb index 92694a7..cb80e91 100644 --- a/epytope/tutorials/EpitopePrediction.ipynb +++ b/epytope/tutorials/EpitopePrediction.ipynb @@ -28,17 +28,14 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 1, "metadata": {}, "outputs": [ { - "ename": "", - "evalue": "", - "output_type": "error", - "traceback": [ - "\u001b[1;31mRunning cells with 'epytope' requires the ipykernel package.\n", - "\u001b[1;31mRun the following command to install 'ipykernel' into the Python environment. \n", - "\u001b[1;31mCommand: 'conda install -n epytope ipykernel --update-deps --force-reinstall'" + "name": "stderr", + "output_type": "stream", + "text": [ + "Using TensorFlow backend.\n" ] } ], From dfa159aa569a0144a0f1a1e378cd24865b974503 Mon Sep 17 00:00:00 2001 From: Jonas Scheid <43858870+jonasscheid@users.noreply.github.com> Date: Wed, 13 Dec 2023 10:10:29 +0100 Subject: [PATCH 3/7] Update CHANGELOG.md Co-authored-by: Christopher Mohr --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index c8996d7..49622bd 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,7 +3,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). -## v3.3.2 - 2023-12-15 +## v3.4.0 - 2023-12-12 ### `Added` From 1cbd169192c1433512301ea93026d4bedd215c34 Mon Sep 17 00:00:00 2001 From: Jonas Scheid <43858870+jonasscheid@users.noreply.github.com> Date: Wed, 13 Dec 2023 10:10:41 +0100 Subject: [PATCH 4/7] Update CHANGELOG.md Co-authored-by: Christopher Mohr --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 49622bd..c83b9f7 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -8,7 +8,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### `Added` - [#93](https://github.com/KohlbacherLab/epytope/pull/93) Added NetMHCIIpan version 4.2 interface [#92](https://github.com/KohlbacherLab/epytope/issues/92) -- [#96](https://github.com/KohlbacherLab/epytope/pull/93) Added NetMHCIIpan version 4.3 interface [#95](https://github.com/KohlbacherLab/epytope/issues/95) +- [#96](https://github.com/KohlbacherLab/epytope/pull/96) Added NetMHCIIpan version 4.3 interface [#95](https://github.com/KohlbacherLab/epytope/issues/95) ### `Changed` From 6512e8a03b2118c3e4f7b0eb80869ff494d1b5ae Mon Sep 17 00:00:00 2001 From: Jonas Scheid <43858870+jonasscheid@users.noreply.github.com> Date: Wed, 13 Dec 2023 10:12:25 +0100 Subject: [PATCH 5/7] Update setup.py Co-authored-by: Christopher Mohr --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index 08c327a..4150a2e 100644 --- a/setup.py +++ b/setup.py @@ -21,7 +21,7 @@ name='epytope', # Version: - version='3.3.2', + version='3.4.0', description='A Framework for Epitope Detection and Vaccine Design', long_description=long_description, From 2d7c73a5e8af5ffa322602ea0a92f74d4528dc8b Mon Sep 17 00:00:00 2001 From: Jonas Scheid <43858870+jonasscheid@users.noreply.github.com> Date: Wed, 13 Dec 2023 10:12:32 +0100 Subject: [PATCH 6/7] Update setup.py Co-authored-by: Christopher Mohr --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index 4150a2e..1e71d0d 100644 --- a/setup.py +++ b/setup.py @@ -32,7 +32,7 @@ # Author details author='Benjamin Schubert, Mathias Walzer, Christopher Mohr, Leon Kuchenbecker', - author_email='benjamin.schubert@helmholtz-muenchen.de, walzer@ebi.ac.uk, christopher.mohr@uni-tuebingen.de, leon.kuchenbecker@uni-tuebingen.de ', + author_email='benjamin.schubert@helmholtz-muenchen.de, walzer@ebi.ac.uk, contact.cmohr@gmail.com, leon.kuchenbecker@uni-tuebingen.de ', # maintainer details maintainer='Christopher Mohr, Jonas Scheid', From ce31c8115a247d114744bfd38e67c472230b77f2 Mon Sep 17 00:00:00 2001 From: Jonas Scheid <43858870+jonasscheid@users.noreply.github.com> Date: Wed, 13 Dec 2023 10:15:46 +0100 Subject: [PATCH 7/7] Update README.md --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 284a987..949e936 100644 --- a/README.md +++ b/README.md @@ -63,7 +63,7 @@ Currently **epytope** provides implementations of several prediction methods or - [NetMHC](https://pubmed.ncbi.nlm.nih.gov/26515819/) 3.0, 3.4, 4.0 - [NetMHCII](https://pubmed.ncbi.nlm.nih.gov/29315598/) 2.2, 2.3 - [NetMHCpan](https://pubmed.ncbi.nlm.nih.gov/28978689/) 2.4, 2.8, 3.0, 4.0, 4.1 - - [NetMHCIIpan](https://pubmed.ncbi.nlm.nih.gov/32406916/) 3.0, 3.1, 4.0, 4.1, 4.2, 4.3 + - [NetMHCIIpan](https://pubmed.ncbi.nlm.nih.gov/38000035/) 3.0, 3.1, 4.0, 4.1, 4.2, 4.3 - [PickPocket](https://pubmed.ncbi.nlm.nih.gov/19297351/) 1.1 - [NetCTLpan](https://pubmed.ncbi.nlm.nih.gov/20379710/) 1.1 - Epitope Selection