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Merge pull request #208 from MannLabs/development
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‎.bumpversion.cfg‎

Lines changed: 20 additions & 8 deletions
Original file line numberDiff line numberDiff line change
@@ -1,5 +1,5 @@
11
[bumpversion]
2-
current_version = 1.2.1
2+
current_version = 1.3.0
33
commit = True
44
tag = False
55
parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)(\-(?P<release>[a-z]+)(?P<build>\d+))?
@@ -15,18 +15,30 @@ serialize =
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1616
[bumpversion:file:./docs/conf.py]
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18-
[bumpversion:file:./release/one_click_linux_gui/control]
18+
[bumpversion:file:./README.md]
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20-
[bumpversion:file:./release/one_click_linux_gui/create_installer_linux.sh]
20+
[bumpversion:file:./release/linux/control]
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22-
[bumpversion:file:./release/one_click_macos_gui/distribution.xml]
22+
[bumpversion:file:./release/linux/build_installer_linux.sh]
2323

24-
[bumpversion:file:./release/one_click_macos_gui/Info.plist]
24+
[bumpversion:file:./release/linux/build_package_linux.sh]
2525

26-
[bumpversion:file:./release/one_click_macos_gui/create_installer_macos.sh]
26+
[bumpversion:file:./release/linux/create_installer_linux.sh]
2727

28-
[bumpversion:file:./release/one_click_windows_gui/create_installer_windows.sh]
28+
[bumpversion:file:./release/macos/distribution.xml]
2929

30-
[bumpversion:file:./release/one_click_windows_gui/peptdeep_innoinstaller.iss]
30+
[bumpversion:file:./release/macos/Info.plist]
31+
32+
[bumpversion:file:./release/macos/create_installer_macos.sh]
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34+
[bumpversion:file:./release/macos/build_installer_macos.sh]
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36+
[bumpversion:file:./release/macos/build_package_macos.sh]
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[bumpversion:file:./release/windows/create_installer_windows.sh]
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[bumpversion:file:./release/windows/build_installer_windows.ps1]
41+
42+
[bumpversion:file:./release/windows/peptdeep_innoinstaller.iss]
3143
search = {current_version}
3244
replace = {new_version}

‎.github/workflows/pip_installation.yml‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -21,7 +21,7 @@ jobs:
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matrix:
2222
os: [ubuntu-latest, macos-13, windows-latest]
2323
# macOS-latest and macos-latest-xlarge use Arm64, resulting in MPS OOM error in peptdeep
24-
# os: [ubuntu-latest, macOS-latest, windows-latest, macos-latest-xlarge]
24+
# os: [ubuntu-latest, macos-13, macos-latest, windows-latest, macos-latest-xlarge]
2525
uses: ./.github/workflows/_run_tests.yml
2626
with:
2727
os: ${{ matrix.os }}
@@ -34,7 +34,7 @@ jobs:
3434
strategy:
3535
matrix:
3636
os: [ubuntu-latest, macos-13, windows-latest]
37-
# os: [ubuntu-latest, macOS-latest, windows-latest, macos-latest-xlarge]
37+
# os: [ubuntu-latest, macos-13, macos-latest, windows-latest, macos-latest-xlarge]
3838
uses: ./.github/workflows/_run_tests.yml
3939
with:
4040
os: ${{ matrix.os }}

‎.github/workflows/publish_and_release.yml‎

Lines changed: 15 additions & 11 deletions
Original file line numberDiff line numberDiff line change
@@ -1,3 +1,4 @@
1+
# TODO remove with old release workflow
12
on:
23
# push:
34
# branches: [ main ]
@@ -57,20 +58,20 @@ jobs:
5758
- name: Creating installer for Linux
5859
shell: bash -l {0}
5960
run: |
60-
cd release/one_click_linux_gui
61+
cd release/linux
6162
. ./create_installer_linux.sh CPU
6263
- name: Test installer for Linux
6364
shell: bash -l {0}
6465
run: |
65-
sudo dpkg -i release/one_click_linux_gui/dist/peptdeep_gui_installer_linux.deb
66+
sudo dpkg -i release/linux/dist/peptdeep_gui_installer_linux.deb
6667
- name: Upload Linux Installer
6768
id: upload-release-asset
6869
uses: actions/upload-release-asset@v1
6970
env:
7071
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
7172
with:
7273
upload_url: ${{ needs.Create_Draft_On_GitHub.outputs.upload_url }}
73-
asset_path: release/one_click_linux_gui/dist/peptdeep_gui_installer_linux.deb
74+
asset_path: release/linux/dist/peptdeep_gui_installer_linux.deb
7475
asset_name: peptdeep_gui_installer_linux.deb
7576
asset_content_type: application/octet-stream
7677
Create_MacOS_Release:
@@ -89,25 +90,27 @@ jobs:
8990
- name: Creating installer for MacOS
9091
shell: bash -l {0}
9192
run: |
92-
cd release/one_click_macos_gui
93+
cd release/macos
9394
. ./create_installer_macos.sh
9495
- name: Test installer for MacOS
9596
shell: bash -l {0}
9697
run: |
97-
sudo installer -pkg release/one_click_macos_gui/dist/peptdeep_gui_installer_macos.pkg -target /
98+
sudo installer -pkg release/macos/dist/peptdeep_gui_installer_macos.pkg -target /
9899
- name: Upload MacOS Installer
99100
id: upload-release-asset
100101
uses: actions/upload-release-asset@v1
101102
env:
102103
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
103104
with:
104105
upload_url: ${{ needs.Create_Draft_On_GitHub.outputs.upload_url }}
105-
asset_path: release/one_click_macos_gui/dist/peptdeep_gui_installer_macos.pkg
106+
asset_path: release/macos/dist/peptdeep_gui_installer_macos.pkg
106107
asset_name: peptdeep_gui_installer_macos.pkg
107108
asset_content_type: application/octet-stream
108109
Create_Windows_Release:
109110
runs-on: windows-latest
110111
needs: Create_Draft_On_GitHub
112+
env:
113+
BUILD_NAME: peptdeep-1.2.1-win-x64
111114
steps:
112115
- name: Checkout code
113116
uses: actions/checkout@v3
@@ -121,14 +124,14 @@ jobs:
121124
- name: Creating installer for Windows
122125
shell: bash -l {0}
123126
run: |
124-
cd release/one_click_windows_gui
127+
cd release/windows
125128
. ./create_installer_windows.sh
126129
- name: Test installer for Windows
127130
shell: bash -l {0}
128131
run: |
129-
cd release/one_click_windows_gui/dist/
132+
cd release/windows/dist/
130133
echo "TODO, this test seems to freeze the runner..."
131-
# ./peptdeep_gui_installer_windows.exe //verysilent //log=log.txt //noicons //tasks= //portable=1
134+
# ./peptdeep-${{ needs.Version_Bumped.outputs.version }}-win-x64.exe //verysilent //log=log.txt //noicons //tasks= //portable=1
132135
# cat log.txt
133136
- name: Upload Windows Installer
134137
id: upload-release-asset
@@ -137,9 +140,10 @@ jobs:
137140
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
138141
with:
139142
upload_url: ${{ needs.Create_Draft_On_GitHub.outputs.upload_url }}
140-
asset_path: release/one_click_windows_gui/dist/peptdeep_gui_installer_windows.exe
141-
asset_name: peptdeep_gui_installer_windows.exe
143+
asset_path: release/windows/dist/peptdeep-${{ needs.Version_Bumped.outputs.version }}-win-x64.exe
144+
asset_name: peptdeep-${{ needs.Version_Bumped.outputs.version }}-win-x64.exe
142145
asset_content_type: application/octet-stream
146+
143147
Create_PyPi_Release:
144148
runs-on: ubuntu-latest
145149
needs: Version_Bumped

‎.github/workflows/release_installers.yml‎

Lines changed: 17 additions & 14 deletions
Original file line numberDiff line numberDiff line change
@@ -1,3 +1,4 @@
1+
# TODO remove with old release workflow
12
on:
23
workflow_dispatch:
34

@@ -54,20 +55,20 @@ jobs:
5455
- name: Creating installer for Linux
5556
shell: bash -l {0}
5657
run: |
57-
cd release/one_click_linux_gui
58+
cd release/linux
5859
. ./create_installer_linux.sh CPU
5960
- name: Test installer for Linux
6061
shell: bash -l {0}
6162
run: |
62-
sudo dpkg -i release/one_click_linux_gui/dist/peptdeep_gui_installer_linux.deb
63+
sudo dpkg -i release/linux/dist/peptdeep_gui_installer_linux.deb
6364
- name: Upload Linux Installer
6465
id: upload-release-asset
6566
uses: actions/upload-release-asset@v1
6667
env:
6768
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
6869
with:
6970
upload_url: ${{ needs.Create_Draft_On_GitHub.outputs.upload_url }}
70-
asset_path: release/one_click_linux_gui/dist/peptdeep_gui_installer_linux.deb
71+
asset_path: release/linux/dist/peptdeep_gui_installer_linux.deb
7172
asset_name: peptdeep_gui_installer_linux.deb
7273
asset_content_type: application/octet-stream
7374
Create_MacOS_Release:
@@ -86,20 +87,20 @@ jobs:
8687
- name: Creating installer for MacOS
8788
shell: bash -l {0}
8889
run: |
89-
cd release/one_click_macos_gui
90+
cd release/macos
9091
. ./create_installer_macos.sh
9192
- name: Test installer for MacOS
9293
shell: bash -l {0}
9394
run: |
94-
sudo installer -pkg release/one_click_macos_gui/dist/peptdeep_gui_installer_macos.pkg -target /
95+
sudo installer -pkg release/macos/dist/peptdeep_gui_installer_macos.pkg -target /
9596
- name: Upload MacOS Installer
9697
id: upload-release-asset
9798
uses: actions/upload-release-asset@v1
9899
env:
99100
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
100101
with:
101102
upload_url: ${{ needs.Create_Draft_On_GitHub.outputs.upload_url }}
102-
asset_path: release/one_click_macos_gui/dist/peptdeep_gui_installer_macos.pkg
103+
asset_path: release/macos/dist/peptdeep_gui_installer_macos.pkg
103104
asset_name: peptdeep_gui_installer_macos.pkg
104105
asset_content_type: application/octet-stream
105106
Create_MacOS_Arm_Release:
@@ -118,25 +119,27 @@ jobs:
118119
- name: Creating installer for MacOS
119120
shell: bash -l {0}
120121
run: |
121-
cd release/one_click_macos_gui
122+
cd release/macos
122123
. ./create_installer_macos.sh
123124
- name: Test installer for MacOS
124125
shell: bash -l {0}
125126
run: |
126-
sudo installer -pkg release/one_click_macos_gui/dist/peptdeep_gui_installer_macos.pkg -target /
127+
sudo installer -pkg release/macos/dist/peptdeep_gui_installer_macos.pkg -target /
127128
- name: Upload MacOS Installer
128129
id: upload-release-asset
129130
uses: actions/upload-release-asset@v1
130131
env:
131132
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
132133
with:
133134
upload_url: ${{ needs.Create_Draft_On_GitHub.outputs.upload_url }}
134-
asset_path: release/one_click_macos_gui/dist/peptdeep_gui_installer_macos.pkg
135+
asset_path: release/macos/dist/peptdeep_gui_installer_macos.pkg
135136
asset_name: peptdeep_gui_installer_macos_arm.pkg
136137
asset_content_type: application/octet-stream
137138
Create_Windows_Release:
138139
runs-on: windows-latest
139140
needs: Create_Draft_On_GitHub
141+
env:
142+
BUILD_NAME: peptdeep-1.2.1-win-x64
140143
steps:
141144
- name: Checkout code
142145
uses: actions/checkout@v3
@@ -150,14 +153,14 @@ jobs:
150153
- name: Creating installer for Windows
151154
shell: bash -l {0}
152155
run: |
153-
cd release/one_click_windows_gui
156+
cd release/windows
154157
. ./create_installer_windows.sh
155158
- name: Test installer for Windows
156159
shell: bash -l {0}
157160
run: |
158-
cd release/one_click_windows_gui/dist/
161+
cd release/windows/dist/
159162
echo "TODO, this test seems to freeze the runner..."
160-
# ./peptdeep_gui_installer_windows.exe //verysilent //log=log.txt //noicons //tasks= //portable=1
163+
# ./peptdeep-1.2.1-win-x64.exe //verysilent //log=log.txt //noicons //tasks= //portable=1
161164
# cat log.txt
162165
- name: Upload Windows Installer
163166
id: upload-release-asset
@@ -166,6 +169,6 @@ jobs:
166169
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
167170
with:
168171
upload_url: ${{ needs.Create_Draft_On_GitHub.outputs.upload_url }}
169-
asset_path: release/one_click_windows_gui/dist/peptdeep_gui_installer_windows.exe
170-
asset_name: peptdeep_gui_installer_windows.exe
172+
asset_path: release/windows/dist/peptdeep-${{ needs.Version_Bumped.outputs.version }}-win-x64.exe
173+
asset_name: peptdeep-${{ needs.Version_Bumped.outputs.version }}-win-x64.exe
171174
asset_content_type: application/octet-stream

‎.gitignore‎

Lines changed: 10 additions & 16 deletions
Original file line numberDiff line numberDiff line change
@@ -1,3 +1,11 @@
1+
# User defined:
2+
peptdeep/logs
3+
*.DS_Store
4+
*sandbox*
5+
*installed_models*
6+
*.last_checked*
7+
*mono_crash.*.blob
8+
19
# Byte-compiled / optimized / DLL files
210
__pycache__/
311
*.py[cod]
@@ -26,6 +34,8 @@ share/python-wheels/
2634
.installed.cfg
2735
*.egg
2836
MANIFEST
37+
dist_pyinstaller/
38+
build_pyinstaller/
2939

3040
# PyInstaller
3141
# Usually these files are written by a python script from a template
@@ -128,19 +138,3 @@ dmypy.json
128138

129139
# Pyre type checker
130140
.pyre/
131-
132-
# User defined:
133-
peptdeep/logs
134-
*.DS_Store
135-
*sandbox*
136-
*installed_models*
137-
*.last_checked*
138-
139-
# nbdev2
140-
*.gitattributes
141-
_docs*
142-
# *_quarto.yml
143-
# *sidebar.yml
144-
*_proc*
145-
# .gitconfig is now autogenerated
146-
.gitconfig

‎.pre-commit-config.yaml‎

Lines changed: 4 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -7,10 +7,10 @@ repos:
77
- id: check-yaml
88
- id: end-of-file-fixer
99
- id: trailing-whitespace
10-
# - repo: https://github.com/astral-sh/ruff-pre-commit
11-
# rev: v0.4.0
12-
# hooks:
13-
# - id: ruff-format
10+
- repo: https://github.com/astral-sh/ruff-pre-commit
11+
rev: v0.5.0
12+
hooks:
13+
- id: ruff-format
1414
# - id: ruff
1515

1616
exclude: .bumpversion.cfg

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