Merge pull request #151 from MannLabs/development

Development

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 1.1.7
+current_version = 1.1.8
 commit = True
 tag = False
 parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)(\-(?P<release>[a-z]+)(?P<build>\d+))?

.github/workflows/release_installers.yml

@@ -102,6 +102,38 @@ jobs:
           asset_path: release/one_click_macos_gui/dist/peptdeep_gui_installer_macos.pkg
           asset_name: peptdeep_gui_installer_macos.pkg
           asset_content_type: application/octet-stream
+  Create_MacOS_Arm_Release:
+    runs-on: macos-latest-xlarge
+    needs: Create_Draft_On_GitHub
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v3
+      - uses: conda-incubator/setup-miniconda@v2
+        with:
+          auto-update-conda: true
+          python-version: ${{ matrix.python-version }}
+      - name: Conda info
+        shell: bash -l {0}
+        run: conda info
+      - name: Creating installer for MacOS
+        shell: bash -l {0}
+        run: |
+          cd release/one_click_macos_gui
+          . ./create_installer_macos.sh
+      - name: Test installer for MacOS
+        shell: bash -l {0}
+        run: |
+          sudo installer -pkg release/one_click_macos_gui/dist/peptdeep_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/peptdeep_gui_installer_macos.pkg
+          asset_name: peptdeep_gui_installer_macos_arm.pkg
+          asset_content_type: application/octet-stream
   Create_Windows_Release:
     runs-on: windows-latest
     needs: Create_Draft_On_GitHub

docs/conf.py

@@ -23,7 +23,7 @@
 copyright = '2022, Mann Labs, MPIB'
 author = 'Mann Labs, MPIB'
 
-release = "1.1.7"
+release = "1.1.8"
 
 # -- General configuration ---------------------------------------------------
 

peptdeep/__init__.py

@@ -11,7 +11,7 @@
 #     pass
 
 __project__ = "peptdeep"
-__version__ = "1.1.7"
+__version__ = "1.1.8"
 __license__ = "Apache 2.0"
 __description__ = "The AlphaX deep learning framework for Proteomics"
 __author__ = "Mann Labs"

peptdeep/model/building_block.py

@@ -594,10 +594,10 @@ def forward(self,
     ):
         mod_x = self.mod_nn(mod_x)
         x = self.aa_emb(aa_indices)
-        charge_x = charges.unsqueeze(1).repeat(
+        charge_x = charges[:, None, None].repeat(
             1, mod_x.size(1), self.charge_dim
         )
-        return self.pos_encoder(torch.cat((x, mod_x,charge_x), 2))
+        return self.pos_encoder(torch.cat((x, mod_x, charge_x), 2))
 
 class Input_26AA_Mod_LSTM(torch.nn.Module):
     """

peptdeep/model/model_interface.py

@@ -39,9 +39,15 @@ def _get_cosine_schedule_with_warmup_lr_lambda(
     current_step: int, *, num_warmup_steps: int, num_training_steps: int, num_cycles: float
 ):
     if current_step < num_warmup_steps:
-        return float(current_step) / float(max(1, num_warmup_steps))
-    progress = float(current_step - num_warmup_steps) / float(max(1, num_training_steps - num_warmup_steps))
-    return max(0.0, 0.5 * (1.0 + math.cos(math.pi * float(num_cycles) * 2.0 * progress)))
+        return float(current_step+1) / float(max(1, num_warmup_steps))
+    progress = float(current_step - num_warmup_steps) / float(num_training_steps - num_warmup_steps)
+    return (
+        max(1e-10, 0.5 * (1.0 + math.cos(math.pi * float(num_cycles) * 2.0 * progress)))
+    )
+    # if current_step < num_warmup_steps:
+    #     return float(current_step) / float(max(1, num_warmup_steps))
+    # progress = float(current_step - num_warmup_steps) / float(max(1, num_training_steps - num_warmup_steps))
+    # return max(0.0, 0.5 * (1.0 + math.cos(math.pi * float(num_cycles) * 2.0 * progress)))
 
 
 def get_cosine_schedule_with_warmup(

peptdeep/utils/_pyinstaller_hooks.py

@@ -0,0 +1,18 @@
+from transformers.dependency_versions_check import pkgs_to_check_at_runtime
+
+def get_peptdeep_datas():
+    """
+    Huggingface has some dependencies those are not included in pyinstaller, 
+    so we need to add them manually.
+    Usages:
+    In pyinstaller's *.spec file, add `datas += get_peptdeep_datas()` before 
+    `.. = Analysis(..., datas=datas,...)`.
+    """
+    from PyInstaller.utils.hooks import copy_metadata
+    for _pkg in ["python","accelerate"]:
+        if _pkg in pkgs_to_check_at_runtime:
+            pkgs_to_check_at_runtime.remove(_pkg)
+    datas = []
+    for _pkg in pkgs_to_check_at_runtime:
+        datas += copy_metadata(_pkg)
+    return datas

release/one_click_linux_gui/control

@@ -1,5 +1,5 @@
 Package: peptdeep
-Version: 1.1.7
+Version: 1.1.8
 Architecture: all
 Maintainer: Mann Labs <opensource@alphapept.com>
 Description: peptdeep

release/one_click_linux_gui/create_installer_linux.sh

@@ -17,7 +17,7 @@ python setup.py sdist bdist_wheel
 # Setting up the local package
 cd release/one_click_linux_gui
 # Make sure you include the required extra packages and always use the stable or very-stable options!
-pip install "../../dist/peptdeep-1.1.7-py3-none-any.whl[stable]"
+pip install "../../dist/peptdeep-1.1.8-py3-none-any.whl[stable]"
 
 if [ "$1" == "CPU" ]; then
     pip install torch -U --extra-index-url https://download.pytorch.org/whl/cpu

release/one_click_macos_gui/Info.plist

@@ -9,9 +9,9 @@
 	<key>CFBundleIconFile</key>
 	<string>alpha_logo.icns</string>
 	<key>CFBundleIdentifier</key>
-	<string>peptdeep.1.1.7</string>
+	<string>peptdeep.1.1.8</string>
 	<key>CFBundleShortVersionString</key>
-	<string>1.1.7</string>
+	<string>1.1.8</string>
 	<key>CFBundleInfoDictionaryVersion</key>
 	<string>6.0</string>
 	<key>CFBundleName</key>

release/one_click_macos_gui/create_installer_macos.sh

@@ -20,7 +20,7 @@ python setup.py sdist bdist_wheel
 
 # Setting up the local package
 cd release/one_click_macos_gui
-pip install "../../dist/peptdeep-1.1.7-py3-none-any.whl[stable]"
+pip install "../../dist/peptdeep-1.1.8-py3-none-any.whl[stable]"
 
 # Creating the stand-alone pyinstaller folder
 pip install pyinstaller
@@ -40,5 +40,5 @@ cp ../../LICENSE.txt Resources/LICENSE.txt
 cp ../logos/alpha_logo.png Resources/alpha_logo.png
 chmod 777 scripts/*
 
-pkgbuild --root dist/peptdeep --identifier de.mpg.biochem.peptdeep.app --version 1.1.7 --install-location /Applications/peptdeep.app --scripts scripts peptdeep.pkg
+pkgbuild --root dist/peptdeep --identifier de.mpg.biochem.peptdeep.app --version 1.1.8 --install-location /Applications/peptdeep.app --scripts scripts peptdeep.pkg
 productbuild --distribution distribution.xml --resources Resources --package-path peptdeep.pkg dist/peptdeep_gui_installer_macos.pkg

release/one_click_macos_gui/distribution.xml

@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="utf-8" standalone="no"?>
 <installer-script minSpecVersion="1.000000">
-    <title>peptdeep 1.1.7</title>
+    <title>peptdeep 1.1.8</title>
     <background mime-type="image/png" file="alpha_logo.png" scaling="proportional"/>
     <welcome file="welcome.html" mime-type="text/html" />
     <conclusion file="conclusion.html" mime-type="text/html" />

release/one_click_windows_gui/create_installer_windows.sh

@@ -17,7 +17,7 @@ python setup.py sdist bdist_wheel
 # Setting up the local package
 cd release/one_click_windows_gui
 # Make sure you include the required extra packages and always use the stable or very-stable options!
-pip install "../../dist/peptdeep-1.1.7-py3-none-any.whl[stable]"
+pip install "../../dist/peptdeep-1.1.8-py3-none-any.whl[stable]"
 
 # Creating the stand-alone pyinstaller folder
 pip install pyinstaller

release/one_click_windows_gui/peptdeep_innoinstaller.iss

@@ -2,7 +2,7 @@
 ; SEE THE DOCUMENTATION FOR DETAILS ON CREATING INNO SETUP SCRIPT FILES!
 
 #define MyAppName "peptdeep"
-#define MyAppVersion "1.1.7"
+#define MyAppVersion "1.1.8"
 #define MyAppPublisher "Max Planck Institute of Biochemistry and the University of Copenhagen, Mann Labs"
 #define MyAppURL "https://github.com/MannLabs/peptdeep"
 #define MyAppExeName "peptdeep_gui.exe"

release/pyinstaller/peptdeep.spec

@@ -10,6 +10,7 @@ import pkg_resources
 import importlib.metadata
 from transformers.dependency_versions_check import pkgs_to_check_at_runtime
 import peptdeep
+from peptdeep.utils._pyinstaller_hooks import get_peptdeep_datas
 
 
 ##################### User definitions
@@ -92,11 +93,7 @@ datas = [d for d in datas if ("__pycache__" not in d[0]) and (d[1] not in [".",
 #	if not os.path.exists(libssl_dll_path):
 #		datas.append((libssl_lib_path, "."))
 
-for _pkg in ["python","accelerate"]:
-	if _pkg in pkgs_to_check_at_runtime:
-		pkgs_to_check_at_runtime.remove(_pkg)
-for _pkg in pkgs_to_check_at_runtime:
-	datas += copy_metadata(_pkg)
+datas += get_peptdeep_datas()
 
 gui_a = Analysis(
 	[gui_script],

settings.ini

@@ -5,7 +5,7 @@
 ### Python library ###
 repo = alphapeptdeep
 lib_name = peptdeep
-version = 1.1.7
+version = 1.1.8
 min_python = 3.7
 license = apache2