Merge pull request #5 from MannLabs/development

Development

.github/ISSUE_TEMPLATE/bug-report.md

@@ -8,7 +8,7 @@ assignees: ''
 ---
 
 **Describe the bug**
-Make sure your bug is not addressed in the [troubleshooting section](https://github.com/MannLabs/py_diaid#troubleshooting) or in [previous issues](https://github.com/MannLabs/py_diaid/issues?q=is%3Aissue). If not, provide a clear and concise description of what the bug is.
+Make sure your bug is not addressed in the [troubleshooting section](https://github.com/MannLabs/pydiaid#troubleshooting) or in [previous issues](https://github.com/MannLabs/pydiaid/issues?q=is%3Aissue). If not, provide a clear and concise description of what the bug is.
 
 **To Reproduce**
 Steps to reproduce the behavior:
@@ -37,7 +37,7 @@ If applicable, add screenshots to help explain your problem.
      - processor [e.g. i386]
      - cpu count [e.g. 8]
    - Python information:
-     - py_diaid version [e.g. 0.1.2]
+     - pydiaid version [e.g. 0.1.2]
      - [other packages]
 
 **Additional context**

.github/workflows/publish_and_release.yml

@@ -62,16 +62,16 @@ jobs:
       - name: Test installer for Linux
         shell: bash -l {0}
         run: |
-          sudo dpkg -i release/one_click_linux_gui/dist/py_diaid_gui_installer_linux.deb
+          sudo dpkg -i release/one_click_linux_gui/dist/pydiaid_gui_installer_linux.deb
       - name: Upload Linux Installer
         id: upload-release-asset
         uses: actions/upload-release-asset@v1
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
         with:
           upload_url: ${{ needs.Create_Draft_On_GitHub.outputs.upload_url }}
-          asset_path: release/one_click_linux_gui/dist/py_diaid_gui_installer_linux.deb
-          asset_name: py_diaid_gui_installer_linux.deb
+          asset_path: release/one_click_linux_gui/dist/pydiaid_gui_installer_linux.deb
+          asset_name: pydiaid_gui_installer_linux.deb
           asset_content_type: application/octet-stream
   Create_MacOS_Release:
     runs-on: macos-latest
@@ -94,16 +94,16 @@ jobs:
       - name: Test installer for MacOS
         shell: bash -l {0}
         run: |
-          sudo installer -pkg release/one_click_macos_gui/dist/py_diaid_gui_installer_macos.pkg -target /
+          sudo installer -pkg release/one_click_macos_gui/dist/pydiaid_gui_installer_macos.pkg -target /
       - name: Upload MacOS Installer
         id: upload-release-asset
         uses: actions/upload-release-asset@v1
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
         with:
           upload_url: ${{ needs.Create_Draft_On_GitHub.outputs.upload_url }}
-          asset_path: release/one_click_macos_gui/dist/py_diaid_gui_installer_macos.pkg
-          asset_name: py_diaid_gui_installer_macos.pkg
+          asset_path: release/one_click_macos_gui/dist/pydiaid_gui_installer_macos.pkg
+          asset_name: pydiaid_gui_installer_macos.pkg
           asset_content_type: application/octet-stream
   Create_Windows_Release:
     runs-on: windows-latest
@@ -128,7 +128,7 @@ jobs:
         run: |
           cd release/one_click_windows_gui/dist/
           echo "TODO, this test seems to freeze the runner..."
-          # ./py_diaid_gui_installer_windows.exe //verysilent //log=log.txt //noicons //tasks= //portable=1
+          # ./pydiaid_gui_installer_windows.exe //verysilent //log=log.txt //noicons //tasks= //portable=1
           # cat log.txt
       - name: Upload Windows Installer
         id: upload-release-asset
@@ -137,8 +137,8 @@ jobs:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
         with:
           upload_url: ${{ needs.Create_Draft_On_GitHub.outputs.upload_url }}
-          asset_path: release/one_click_windows_gui/dist/py_diaid_gui_installer_windows.exe
-          asset_name: py_diaid_gui_installer_windows.exe
+          asset_path: release/one_click_windows_gui/dist/pydiaid_gui_installer_windows.exe
+          asset_name: pydiaid_gui_installer_windows.exe
           asset_content_type: application/octet-stream
   Create_PyPi_Release:
     runs-on: ubuntu-latest

.gitignore

@@ -129,10 +129,9 @@ dmypy.json
 .pyre/
 
 # User defined:
-py_diaid/logs
+pydiaid/logs
 *.DS_Store
 *sandbox*
-py_diaid/input
-py_diaid/static
-py_diaid/lib
-output_py_diaid
+pydiaid/input
+pydiaid/static/AlphaPept_results.csv
+output_pydiaid

MANIFEST.in

@@ -1,4 +1,4 @@
-recursive-include py_diaid *
+recursive-include pydiaid *
 include LICENSE.txt
 include README.md
-recursive-exclude py_diaid/logs *
+recursive-exclude pydiaid/logs *

misc/bumpversion.cfg

@@ -1,17 +1,17 @@
 [bumpversion]
-current_version = 0.0.3
+current_version = 0.0.14
 commit = True
 tag = False
 parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)(\-(?P<release>[a-z]+)(?P<build>\d+))?
-serialize =
+serialize = 
 	{major}.{minor}.{patch}
 	{major}.{minor}.{patch}
 
 [bumpversion:part:release]
 
 [bumpversion:part:build]
 
-[bumpversion:file:../py_diaid/__init__.py]
+[bumpversion:file:../pydiaid/__init__.py]
 
 [bumpversion:file:../release/one_click_linux_gui/control]
 
@@ -25,6 +25,6 @@ serialize =
 
 [bumpversion:file:../release/one_click_windows_gui/create_installer_windows.sh]
 
-[bumpversion:file:../release/one_click_windows_gui/py_diaid_innoinstaller.iss]
+[bumpversion:file:../release/one_click_windows_gui/pydiaid_innoinstaller.iss]
 search = {current_version}
 replace = {new_version}

misc/check_version.sh

@@ -1,9 +1,9 @@
-current_version=$(grep "__version__" ../py_diaid/__init__.py | cut -f3 -d ' ' | sed 's/"//g')
+current_version=$(grep "__version__" ../pydiaid/__init__.py | cut -f3 -d ' ' | sed 's/"//g')
 current_version_as_regex=$(echo $current_version | sed 's/\./\\./g')
 conda create -n version_check python=3.8 pip=20.1 -y
 conda activate version_check
 set +e
-already_on_pypi=$(pip install py_diaid== 2>&1 | grep -c "$current_version_as_regex")
+already_on_pypi=$(pip install pydiaid== 2>&1 | grep -c "$current_version_as_regex")
 set -e
 conda deactivate
 if [ $already_on_pypi -ne 0 ]; then

misc/loose_pip_install.sh

@@ -1,5 +1,5 @@
-conda create -n py_diaid python=3.8 -y
-conda activate py_diaid
+conda create -n pydiaid python=3.8 -y
+conda activate pydiaid
 pip install -e '../.[development]'
-py_diaid
+pydiaid
 conda deactivate

misc/stable_pip_install.sh

@@ -1,5 +1,5 @@
-conda create -n py_diaid python=3.8 -y
-conda activate py_diaid
+conda create -n pydiaid python=3.8 -y
+conda activate pydiaid
 pip install -e '../.[stable,development-stable]'
-py_diaid
+pydiaid
 conda deactivate