Version 1.1.7 (#471)

* single click to trigger jump to metabolite * Bump to 1.1.7 Co-authored-by: axelvonkamp <[email protected]>
cnapy-org · May 9, 2023 · dcaead5 · dcaead5
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diff --git a/README.md b/README.md
@@ -59,7 +59,7 @@ Everyone is welcome to contribute to CNApy's development. [See our contribution
 
 ## Using the Windows installer
 
-1. Download the zipped CNApy Windows installer [from here](https://github.com/cnapy-org/CNApy/releases/download/v1.1.6/cnapy-windows-installer.zip).
+1. Download the zipped CNApy Windows installer [from here](https://github.com/cnapy-org/CNApy/releases/download/v1.1.7/cnapy-windows-installer.zip).
 2. Unzip the file into your desired location. You can do this by right-clicking on the file and selecting the option to extract the files.
 3. In the location where you unzipped the file, click on "INSTALL_CNAPY.bat". As soon as the installation is finished, the appearing window closes and you can start CNApy either by double-clicking on the newly created CNApy desktop icon or by searching for CNApy through the task bar search.
 
@@ -75,12 +75,12 @@ Click on the operating system you use:
 1. Download Miniconda [from here](https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh).
 2. Install Miniconda by double-clicking the downloaded file. If the script does not run, right-click on the file, open its settings and select the option to make it executable (alternative: run 'chmod u+x ./Miniconda3-latest-Linux-x86_64.sh' in your terminal). Follow the appearing installation instructions and remember in which folder you install Miniconda. If you already use Anaconda on your computer (for which we also directly provide a conda CNApy package, [see here](#install-cnapy-as-conda-package)), deactivate all installation options which put Miniconda to your console or system PATH to avoid possible problems.
 3. Using your file manager, go to the folder where you installed Miniconda. Then, open the appearing sub-folder "condabin".
-4. Download the CNApy installation assistant script [from here](https://github.com/cnapy-org/CNApy/releases/download/v1.1.6/cnapy-assistant-script.sh) into the mentioned "condabin" folder.
+4. Download the CNApy installation assistant script [from here](https://github.com/cnapy-org/CNApy/releases/download/v1.1.7/cnapy-assistant-script.sh) into the mentioned "condabin" folder.
 5. In the file manager, double-click on the newly downloaded installation assistant script which is called "cnapy-assistant-script.sh". If the script does not run, right-click on the file, open its settings and select the option to make it executable (alternative: run 'chmod u+x ./cnapy-assistant-script.sh' in your terminal). Wait until CNApy is downloaded and installed.
 6. You can now run CNApy by executing the following two terminal instructions in the mentioned "condabin" folder:
 
 ```sh
-./conda activate cnapy-1.1.6
+./conda activate cnapy-1.1.7
 cnapy
 ```
 
@@ -89,12 +89,12 @@ cnapy
 1. If you have a (new) Mac with an ARM processor, such as the M1 or M2, download Miniconda [from here](https://repo.anaconda.com/miniconda/Miniconda3-latest-MacOSX-arm64.pkg). If you have an (older) Mac with an Intel processor, download Miniconda [from here](https://repo.anaconda.com/miniconda/Miniconda3-latest-MacOSX-x86_64.pkg). If you are unsure which processor your Mac has, click on the Apple menu in the upper-left of your screen and choose "About This Mac".
 2. Install Miniconda by double-clicking the downloaded file. Follow the appearing installation instructions and remember in which folder you install Miniconda. If you already use Anaconda on your computer (for which we directly provide a conda CNApy package, [see here](#install-cnapy-as-conda-package)), deactivate all installation options which put Miniconda to your console or system PATH to avoid possible problems
 3. Using Finder, go to the folder where you installed Miniconda. Then, open the appearing sub-folder "condabin".
-4. Download the CNApy installation assistant script [from here](https://github.com/cnapy-org/CNApy/releases/download/v1.1.6/cnapy-assistant-script.sh) into the mentioned "condabin" folder.
+4. Download the CNApy installation assistant script [from here](https://github.com/cnapy-org/CNApy/releases/download/v1.1.7/cnapy-assistant-script.sh) into the mentioned "condabin" folder.
 5. In the file manager, double-click on the newly downloaded installation assistant script which is called "cnapy-installation-script.sh". If the script does not run, right-click on the file, open its settings and select the option to make it executable (alternative: run 'chmod u+x ./cnapy-assistant-script.sh' in your terminal). Wait until CNApy is downloaded and installed.
 6. Open the terminal in the mentioned "condabin" folder. You can now run CNApy by executing the following two terminal instructions:
 
 ```sh
-./conda activate cnapy-1.1.6
+./conda activate cnapy-1.1.7
 cnapy
 ```
 
@@ -103,13 +103,13 @@ cnapy
 1. Create a conda environment with all dependencies
 
     ```sh
-    conda create -n cnapy-1.1.6 -c Gurobi -c IBMDecisionOptimization -c conda-forge -c cnapy cnapy=1.1.6 --yes
+    conda create -n cnapy-1.1.7 -c Gurobi -c IBMDecisionOptimization -c conda-forge -c cnapy cnapy=1.1.7 --yes
     ```
 
 2. Activate the cnapy conda environment
 
     ```sh
-    conda activate cnapy-1.1.6
+    conda activate cnapy-1.1.7
     ```
 
 3. Run CNApy within you activated conda environment

diff --git a/cnapy/appdata.py b/cnapy/appdata.py
@@ -30,7 +30,7 @@ class AppData:
     ''' The application data '''
 
     def __init__(self):
-        self.version = "cnapy-1.1.6"
+        self.version = "cnapy-1.1.7"
         self.format_version = 2
         self.unsaved = False
         self.project = ProjectData()

diff --git a/cnapy/core.py b/cnapy/core.py
@@ -282,6 +282,7 @@ def element_exchange_balance(model: cobra.Model, scen_values: Scenario, non_boun
             if rxn.boundary:
                 reaction_fluxes.append((rxn, flux))
 
+        metabolites_without_formulas = set()
         for rxn, flux in reaction_fluxes:
             for met, coeff in rxn.metabolites.items():
                 val = coeff * flux
@@ -291,6 +292,8 @@ def element_exchange_balance(model: cobra.Model, scen_values: Scenario, non_boun
                     flux_dict = efflux
                 else:
                     continue
+                if len(met.elements) == 0:
+                    metabolites_without_formulas.add(met.id)
                 for el, count in met.elements.items():
                     if not organic_elements_only or el in organic_elements:
                         flux_dict[el] += count * val
@@ -307,6 +310,10 @@ def print_in_out_balance():
                 elements.remove(el)
         for el in elements:
             print_in_out_balance()
+        if len(metabolites_without_formulas) > 0:
+            print_func("WARNING: Metabolites wihtout formulas encountered:")
+            print_func(", ".join(met for met in metabolites_without_formulas))
+            print_func("The results are likely to be incorrect!")
     return influx, efflux
 
 def check_biomass_weight(model: cobra.Model, bm_reac_id: str) -> float:

diff --git a/cnapy/gui_elements/flux_feasibility_dialog.py b/cnapy/gui_elements/flux_feasibility_dialog.py
@@ -521,8 +521,8 @@ def show_elemental_balance(self):
         elif len(self.bm_reac_id) > 0:
             non_boundary_reactions.append(self.bm_reac_id)
             biomass_text = " including biomass reaction " + self.bm_reac_id
-        def print_to_console(txt):
-            self.main_window.centralWidget().console._append_plain_text(txt + "\n", before_prompt=True)
+        def print_to_console(*txt):
+            self.main_window.centralWidget().console._append_plain_text(' '.join(list(txt)) + "\n", before_prompt=True)
         print_to_console("\nScenario fluxes" + biomass_text + ":")
         element_exchange_balance(self.appdata.project.cobra_py_model, self.appdata.project.scen_values,
                                  non_boundary_reactions, organic_elements_only=True, print_func=print_to_console)

diff --git a/cnapy/gui_elements/reaction_table_widget.py b/cnapy/gui_elements/reaction_table_widget.py
@@ -1,6 +1,7 @@
 from enum import Enum
 from qtpy.QtCore import Qt, Signal, Slot
 from qtpy.QtWidgets import QApplication, QTableWidget, QTableWidgetItem, QAbstractItemView, QPlainTextEdit
+from qtpy.QtGui import QMouseEvent, QTextCursor
 
 
 class ModelElementType(Enum):
@@ -11,23 +12,31 @@ class ModelElementType(Enum):
 class ReactionString(QPlainTextEdit):
     def __init__(self, reaction, metabolite_list):
         super().__init__()
-        reaction_string = reaction.build_reaction_string()
+        reaction_string = reaction.build_reaction_string() + " " # extra space to be able to click outside the equation without triggering a jump to the metabolite
         self.setPlainText(reaction_string)
         self.text_width = self.fontMetrics().horizontalAdvance(reaction_string)
         self.setReadOnly(True)
         self.model = reaction.model
         self.metabolite_list = metabolite_list
-        self.selectionChanged.connect(self.switch_metabolite)
 
     jumpToMetabolite = Signal(str)
 
-    @Slot()
-    def switch_metabolite(self):
-        selected_text = self.textCursor().selectedText()
-        if self.model.metabolites.has_id(selected_text):
-            self.jumpToMetabolite.emit(selected_text)
-            self.metabolite_list.set_current_item(selected_text)
-
+    def mouseReleaseEvent(self, event: QMouseEvent):
+        if event.button() == Qt.LeftButton:
+            text_cursor: QTextCursor = self.textCursor()
+            if not text_cursor.hasSelection():
+                start: int = text_cursor.position()
+                text: str = self.toPlainText()
+                if start >= len(text):
+                    return
+                while start > 0:
+                    start -= 1
+                    if text[start].isspace():
+                        break
+                text = text[start:].split(maxsplit=1)[0]
+                if self.model.metabolites.has_id(text):
+                    self.jumpToMetabolite.emit(text)
+                    self.metabolite_list.set_current_item(text)
 
 class ReactionTableWidget(QTableWidget):
     def __init__(self, appdata, element_type: ModelElementType) -> None:

diff --git a/constructor/linux/construct.yaml b/constructor/linux/construct.yaml
@@ -1,5 +1,5 @@
 name: CNApy
-version: 1.1.6
+version: 1.1.7
 
 ignore_duplicate_files: True
 

diff --git a/constructor/win/README.md b/constructor/win/README.md
@@ -24,12 +24,12 @@ We use conda as package manager to install CNApy. You can use [miniconda](https:
 
 1. Create a conda environment with all dependencies
     ```sh
-    conda create -n cnapy-1.1.6 -c conda-forge -c cnapy cnapy=1.1.6
+    conda create -n cnapy-1.1.7 -c conda-forge -c cnapy cnapy=1.1.7
     ```
 
 2. Activate the cnapy conda environment
     ```
-    conda activate cnapy-1.1.6
+    conda activate cnapy-1.1.7
     ```
 
 3. Run CNApy

diff --git a/constructor/win/construct.yaml b/constructor/win/construct.yaml
@@ -1,5 +1,5 @@
 name: CNApy
-version: 1.1.6
+version: 1.1.7
 
 ignore_duplicate_files: True
 
@@ -10,7 +10,7 @@ channels:
 
 specs:
   - conda
-  # - cnapy=1.1.6
+  # - cnapy=1.1.7
   - mamba
   - pip
   - python=3.8

diff --git a/constructor/win/post_install.bat b/constructor/win/post_install.bat
@@ -1,5 +1,5 @@
 call %~dp0..\Scripts\activate.bat
 
-call mamba install cnapy=1.1.6 -c cnapy -c conda-forge -v --yes
+call mamba install cnapy=1.1.7 -c cnapy -c conda-forge -v --yes
 call pause
 call %~dp0..\Scripts\conda clean --all --yes
diff --git a/docs/index.md b/docs/index.md
@@ -61,13 +61,13 @@ Everyone is welcome to contribute to CNApy's development. [See our contribution
 3. Create a conda environment with all dependencies
 
     ```sh
-    conda create -n cnapy-1.1.6 -c conda-forge -c cnapy cnapy=1.1.6
+    conda create -n cnapy-1.1.7 -c conda-forge -c cnapy cnapy=1.1.7
     ```
 
 4. Activate the cnapy conda environment
 
     ```sh
-    conda activate cnapy-1.1.6
+    conda activate cnapy-1.1.7
     ```
 
 5. Run CNApy within you activated conda environment

diff --git a/recipes/linux/meta.yaml b/recipes/linux/meta.yaml
@@ -1,4 +1,4 @@
-{% set version = '1.1.6' %}
+{% set version = '1.1.7' %}
 
 package:
   name: cnapy

diff --git a/recipes/noarch/meta.yaml b/recipes/noarch/meta.yaml
@@ -1,4 +1,4 @@
-{% set version = '1.1.6' %}
+{% set version = '1.1.7' %}
 
 package:
   name: cnapy

diff --git a/recipes/win/meta.yaml b/recipes/win/meta.yaml
@@ -1,4 +1,4 @@
-{% set version = '1.1.6' %}
+{% set version = '1.1.7' %}
 
 package:
   name: cnapy

diff --git a/setup.py b/setup.py
@@ -18,7 +18,7 @@
 
 setup(
     name='cnapy',
-    version='1.1.6',
+    version='1.1.7',
     url='https://github.com/cnapy-org/CNApy/',
     license='GPLv3+',
     description='An integrated environment for metabolic network analysis.',