Merge remote-tracking branch 'origin/main' into fix-update-of-first-classifier

Author: anna-charlotte

.bumpversion.toml

@@ -1,5 +1,5 @@
 [tool.bumpversion]
-current_version = "1.9.3-dev1"
+current_version = "1.9.3-dev2"
 parse = """(?x)
     (?P<major>0|[1-9]\\d*)\\.
     (?P<minor>0|[1-9]\\d*)\\.

.github/workflows/pip_installation.yml

@@ -8,6 +8,8 @@
 on:
   push:
     branches: [ main ]
+  schedule:
+    - cron: "0 0 * * *"   # daily at midnight, to get feedback on the loose version
   workflow_dispatch:
 
 name: Pip install + unit tests

alphadia/__init__.py

@@ -1,3 +1,3 @@
 #!python
 
-__version__ = "1.9.3-dev1"
+__version__ = "1.9.3-dev2"

alphadia/cli.py

@@ -176,7 +176,11 @@ def _get_raw_path_list_from_args_and_config(
         if re.search(args.regex, os.path.basename(f)) is not None
     ]
     len_after = len(raw_path_list)
-    print(f"Removed {len_before - len_after} of {len_before} files.")
+
+    if len_removed := len_before - len_after:
+        print(
+            f"Ignoring {len_removed} / {len_before} file(s) from arguments list due to --regex."
+        )
 
     return raw_path_list
 

alphadia/constants/default.yaml

@@ -2,6 +2,7 @@
 version: 1
 
 # These values are typically filled via CLI parameters
+workflow_name: null
 output_directory: null
 library_path: null
 raw_paths: []

alphadia/exceptions.py

@@ -27,8 +27,16 @@ def __str__(self):
 class BusinessError(CustomError):
     """Custom error class for 'business' errors.
 
-    A 'business' error is an error that is caused by the input (data, configuration, ...) and not by a
-    malfunction in alphaDIA.
+    A 'business' error is an error that is caused during processing the input (data, configuration, ...) and not by a
+    malfunction in AlphaDIA.
+    """
+
+
+class UserError(CustomError):
+    """Custom error class for 'user' errors.
+
+    A 'user' error is an error that is caused by the incompatible user input (data, configuration, ...) and not by a
+    malfunction in AlphaDIA.
     """
 
 
@@ -64,6 +72,19 @@ class NotDiaDataError(BusinessError):
     _msg = "Could not find cycle shape. Please check if this is a valid DIA data set."
 
 
+class NoLibraryAvailableError(UserError):
+    """Raise when no library is available."""
+
+    _error_code = "NO_LIBRARY_AVAILABLE"
+
+    _msg = "No spectral library available."
+
+    _detail_msg = """No spectral library available.
+
+    Either provide a spectral library file (via GUI, config or command line parameter),
+    or provide a FASTA file and set the "Predict Library" (GUI) / 'library_prediction.predict' (config) flag."""
+
+
 class ConfigError(BusinessError):
     """Raise when something is wrong with the provided configuration."""
 
@@ -73,22 +94,29 @@ class ConfigError(BusinessError):
     _key = ""
     _config_name = ""
 
-    def __init__(self, key: str, config_name: str):
+    def __init__(self, key: str, value: str, config_name: str):
         self._key = key
+        self._value = value
         self._config_name = config_name
 
 
 class KeyAddedConfigError(ConfigError):
     """Raise when a key should be added to a config."""
 
-    def __init__(self, key: str, config_name: str):
-        super().__init__(key, config_name)
-        self._detail_msg = f"Defining new keys is not allowed when updating a config: key='{self._key}', config_name='{self._config_name}'"
+    def __init__(self, key: str, value: str, config_name: str):
+        super().__init__(key, value, config_name)
+        self._detail_msg = (
+            f"Defining new keys is not allowed when updating a config: "
+            f"key='{self._key}', value='{self._value}', config_name='{self._config_name}'"
+        )
 
 
 class TypeMismatchConfigError(ConfigError):
     """Raise when the type of a value does not match the default type."""
 
-    def __init__(self, key: str, config_name: str, extra_msg: str):
-        super().__init__(key, config_name)
-        self._detail_msg = f"Types of values must match default config: key='{self._key}', config_name='{self._config_name}', types='{extra_msg}'"
+    def __init__(self, key: str, value: str, config_name: str, extra_msg: str):
+        super().__init__(key, value, config_name)
+        self._detail_msg = (
+            f"Types of values must match default config: "
+            f"key='{self._key}', value='{self._value}', config_name='{self._config_name}', types='{extra_msg}'"
+        )

alphadia/search_step.py

@@ -10,7 +10,7 @@
 
 from alphadia import libtransform, outputtransform
 from alphadia.constants.keys import ConfigKeys
-from alphadia.exceptions import CustomError
+from alphadia.exceptions import CustomError, NoLibraryAvailableError
 from alphadia.workflow import peptidecentric, reporting
 from alphadia.workflow.base import WorkflowBase
 from alphadia.workflow.config import (
@@ -271,7 +271,8 @@ def get_run_data(self) -> Generator[tuple[str, str, SpecLibFlat]]:
         """Generator for raw data and spectral library."""
 
         if self.spectral_library is None:
-            raise ValueError("no spectral library loaded")
+            # TODO: check alternative: more fine-grained errors could be raised on the level of search_plan
+            raise NoLibraryAvailableError()
 
         # iterate over raw files and yield raw data and spectral library
         for i, raw_location in enumerate(self.raw_path_list):
@@ -340,9 +341,13 @@ def _process_raw_file(
 
         if self.config["general"]["reuse_quant"]:
             if os.path.exists(psm_location) and os.path.exists(frag_location):
-                logger.info(f"Found existing quantification for {raw_name}")
+                logger.info(
+                    f"reuse_quant: found existing quantification for {raw_name}, skipping processing .."
+                )
                 return workflow
-            logger.info(f"No existing quantification found for {raw_name}")
+            logger.info(
+                f"reuse_quant: no existing quantification found for {raw_name}, proceeding with processing .."
+            )
 
         workflow.load(dia_path, speclib)
 

alphadia/workflow/base.py

@@ -56,7 +56,7 @@ def __init__(
         self._quant_path: str = quant_path or os.path.join(
             config[ConfigKeys.OUTPUT_DIRECTORY], QUANT_FOLDER_NAME
         )
-        logger.info(f"Saving quantification results to {self._quant_path}")
+        logger.info(f"Quantification results path: {self._quant_path}")
 
         self._config: Config = config
         self.reporter: reporting.Pipeline | None = None

alphadia/workflow/config.py

@@ -166,7 +166,7 @@ def _update(
     """
     for key, update_value in update_config.items():
         if key not in target_config:
-            raise KeyAddedConfigError(key, config_name)
+            raise KeyAddedConfigError(key, update_value, config_name)
 
         target_value = target_config[key]
         tracking_value = tracking_dict[key]
@@ -180,7 +180,10 @@ def _update(
             )
         ):
             raise TypeMismatchConfigError(
-                key, config_name, f"{type(update_value)} != {type(target_value)}"
+                key,
+                update_value,
+                config_name,
+                f"{type(update_value)} != {type(target_value)}",
             )
 
         if isinstance(target_value, dict):

alphadia/workflow/manager.py

@@ -820,7 +820,9 @@ def load_classifier_store(self, path: None | str = None):
 
                     if classifier_hash not in self.classifier_store:
                         classifier = deepcopy(self.classifier_base)
-                        classifier.from_state_dict(torch.load(os.path.join(path, file)))
+                        classifier.from_state_dict(
+                            torch.load(os.path.join(path, file), weights_only=False)
+                        )
                         self.classifier_store[classifier_hash].append(classifier)
 
     def get_classifier(self, available_columns: list, version: int = -1):

alphadia/workflow/reporting.py

@@ -9,6 +9,7 @@
 import warnings
 from datetime import datetime, timedelta
 from io import BytesIO
+from pathlib import Path
 
 # alphadia imports
 # alpha family imports
@@ -108,9 +109,7 @@ def format(self, record: logging.LogRecord):
         return f"{elapsed} {self.formatter[record.levelno].format(record)}"
 
 
-def init_logging(
-    log_folder: str = None, log_level: int = logging.INFO, overwrite: bool = True
-):
+def init_logging(log_folder: str = None, log_level: int = logging.INFO):
     """Initialize the default logger.
     Sets the formatter and the console and file handlers.
 
@@ -122,9 +121,6 @@ def init_logging(
 
     log_level : int, default logging.INFO
         Log level to use. Can be logging.DEBUG, logging.INFO, logging.WARNING, logging.ERROR or logging.CRITICAL.
-
-    overwrite : bool, default True
-        Whether to overwrite the log file if it already exists.
     """
 
     global __is_initiated__
@@ -147,20 +143,39 @@ def init_logging(
     if log_folder is not None:
         os.makedirs(log_folder, exist_ok=True)
 
-        log_name = os.path.join(log_folder, "log.txt")
-        # check if log file exists
-        if os.path.exists(log_name) and overwrite:
-            # if it does, delete it
-            os.remove(log_name)
+        log_file_path = os.path.join(log_folder, "log.txt")
+
+        moved_log_file_path = _move_old_logs(log_file_path)
+
         # create file handler which logs even debug messages
-        fh = logging.FileHandler(log_name, encoding="utf-8")
+        fh = logging.FileHandler(log_file_path, encoding="utf-8")
         fh.setLevel(log_level)
         fh.setFormatter(DefaultFormatter(use_ansi=False))
         logger.addHandler(fh)
 
+        if moved_log_file_path:
+            logger.info(f"Moved old log file {log_file_path} to {moved_log_file_path}")
+
     __is_initiated__ = True
 
 
+def _move_old_logs(log_file_path: str) -> str | None:
+    """Move old log files to a new name with an incrementing number."""
+    old_path = Path(log_file_path)
+    new_path = old_path
+
+    n = -1
+    while new_path.exists():
+        n += 1
+        new_path = old_path.parent / f"{old_path.stem}.{n}.bkp{old_path.suffix}"
+
+    if n != -1:
+        Path(log_file_path).rename(new_path)
+        return str(new_path)
+
+    return None
+
+
 class Backend:
     """Generic backend for logging metrics, plots and strings.
 

docs/guides/libfree-gui.md

@@ -9,7 +9,8 @@ Also ensure the right execution engine has been selected and your version is up
 <img src="../_static/images/libfree-gui/initial_engine.png" width="100%" height="auto">
 
 ## 2. Project Structure
-We will be performing two DIA searches: a first search for library generation and a second search for joined quantification. To accommodate this, we prepare the project directory to have a `first_pass` and a `second_pass` folder. You can change the project path in the `Output Files` tab
+We will be performing two DIA searches: a first search for library generation and a second search for joined quantification. To accommodate this, we prepare the project directory to have a `first_pass` and a `second_pass` folder,
+which can then be selected in the `Output Files` tab.
 <img src="../_static/images/libfree-gui/initial_folders.png" width="100%" height="auto">
 
 ## 3. First search
@@ -30,7 +31,9 @@ Keeping track of optimized mass tolerance values for different instrument setups
 
 <img src="../_static/images/libfree-gui/first_settings.png" width="100%" height="auto">
 
-Start the first search by clicking the "Run Workflow" button. This will take between one and two hours depending on your system.
+3. In the "Output Files" tab, select the `first_pass` folder as the output directory.
+
+4. Start the first search by clicking the "Run Workflow" button. This will take between one and two hours depending on your system.
 
 ## 4. Second search
 For the second search, we will use the library generated in the first search to quantify precursors across samples. Load all raw files as previously but remove the FASTA file. Instead, select the `speclib.mbr.hdf` as the spectral library.
@@ -40,6 +43,8 @@ For the second search, configure the `thread_count`, `target_ms1_tolerance`, and
 
 <img src="../_static/images/libfree-gui/second_settings.png" width="100%" height="auto">
 
+In the "Output Files" tab, select the `second_pass` folder as the output directory.
+
 Finally, start the search as before. This search will take only around 2 minutes per file.
 
 ## 5. Results

docs/installation.md

@@ -108,6 +108,14 @@ The GUI can then be started by typing
 npm run dev
 ```
 
+Ignore the error message telling you that the `BundledExecutionEngine` is not available
+In order to use the locally installed version, select the `CMDExecutionEngine`in the top bar.
+
+By default, this looks for an AlphaDIA installation in a conda environment called `alphadia`.
+If you want to use a different environment, locate the `profile.json` file
+(MacOS: via "Electron" -> "Settings" in the top menu, e.g. `~/Library/Application Support/alphadia/profile.json`)
+and adjust `CMDExecutionEngine.envName`.
+
 ## Docker Installation
 The containerized version can be used to run alphaDIA e.g. on cloud platforms.
 It can be used to run alphaDIA for multiple input files, as well as for single files only

gui/package.json

@@ -1,7 +1,7 @@
 {
   "name": "alphadia",
   "productName": "alphadia-gui",
-  "version": "1.9.3-dev1",
+  "version": "1.9.3-dev2",
   "description": "Graphical user interface for DIA data analysis",
   "main": "dist/electron.js",
   "homepage": "./",

gui/src/main/modules/engine.js

@@ -307,7 +307,8 @@ function hasBinary(binaryPath){
     return new Promise((resolve, reject) => {
         fs.access(binaryPath, fs.constants.X_OK, (err) => {
             if (err) {
-                reject("hasBinary: Binary " + binaryPath + " not found or not executable.")
+                reject("BundledExecutionEngine: Binary " + binaryPath + " not found or not executable." +
+                    "\n\nYou may use the CMDExecutionEngine instead.")
             } else {
                 resolve()
             }
@@ -367,8 +368,8 @@ class BundledExecutionEngine extends BaseExecutionEngine {
                 BrowserWindow.getFocusedWindow(),
                 {
                     type: 'error',
-                    title: 'Error while checking availability of bundled alphaDIA',
-                    message: `Could not start bundled alphaDIA. ${err}`,
+                    title: 'Error while checking availability of bundled AlphaDIA',
+                    message: `Could not start bundled AlphaDIA.\n${err}`,
                 }).catch((err) => {
                     console.log(err)
                 })

gui/src/main/modules/profile.js

@@ -3,7 +3,7 @@ const path = require("path")
 const { app, shell, BrowserWindow} = require("electron")
 const { dialog } = require('electron')
 
-const VERSION = "1.9.3-dev1"
+const VERSION = "1.9.3-dev2"
 
 const Profile = class {
 

gui/src/main/modules/workflows.js

@@ -76,7 +76,7 @@ function validateWorkflow(workflow) {
 
 function workflowToConfig(workflow) {
 
-    let output = {name: workflow.name}
+    let output = {workflow_name: workflow.name}
 
     if (workflow.library.path != "") {
         output["library_path"] = workflow.library.path

gui/src/renderer/pages/Home.js

@@ -55,7 +55,7 @@ const VersionCard = () => {
         let currentActiveVersion = profile.executionEngines[profile.activeIdx].versions.filter((versionEntry) => versionEntry.name === "alphadia")[0].version
         versionOutput = currentActiveVersion
 
-        if (currentActiveVersion != "1.2.0") {
+        if (currentActiveVersion != "1.2.0") { // TODO fix
             updateOutput = (
                 <Stack direction="row" alignItems="center" gap={1}>
                     <CheckIcon sx={{color:"rgb(75, 211, 26)"}}/>

misc/pip_install.sh

@@ -1,3 +1,8 @@
+#!/bin/bash
+### Install the package with a given type in a defined conda environment with a define python version,
+### and call it to check if it works
+### example usage:
+### ./pip_install.sh stable my_env 3.9
 set -e -u
 
 INSTALL_TYPE=$1 # stable, loose, etc..

release/linux/control

@@ -1,5 +1,5 @@
 Package: alphadia
-Version: 1.9.3-dev1
+Version: 1.9.3-dev2
 Architecture: all
 Maintainer: Mann Labs <opensource@alphapept.com>
 Description: alphadia

release/macos/build_package_macos.sh

@@ -7,10 +7,10 @@ set -e -u
 # Set up package name and version
 PACKAGE_NAME="alphadia"
 APP_NAME="alphadia"
-PACKAGE_VERSION="1.9.3-dev1"
+PACKAGE_VERSION="1.9.3-dev2"
 PKG_FOLDER="dist/$APP_NAME.app"
 
-# BUILD_NAME is taken from environment variables, e.g. alphadia-1.9.3-dev1-macos-darwin-arm64 or alphadia-1.9.3-dev1-macos-darwin-x64
+# BUILD_NAME is taken from environment variables, e.g. alphadia-1.9.3-dev2-macos-darwin-arm64 or alphadia-1.9.3-dev2-macos-darwin-x64
 rm -rf ${BUILD_NAME}.pkg
 
 # Cleanup the package folder