Feature merge2

.github/workflows/choose_branch.yaml

@@ -20,7 +20,7 @@ jobs:
       max-parallel: 5
       fail-fast: false
       matrix:
-        python-version: ["3.8", "3.9", "3.10"]
+        python-version: ["3.10", "3.11", "3.12"]
         platform:
           - { name: "windows", os: "windows-latest", shell: "pwsh" }
           - { name: "linux", os: "ubuntu-latest", shell: "bash -l {0}" }
@@ -30,14 +30,14 @@ jobs:
           # but Linux
           - platform:
               { name: "macos", os: "macos-latest", shell: "bash -l {0}" }
-            python-version: "3.8"
+            python-version: "3.10"
           - platform: { name: "windows", os: "windows-latest", shell: "pwsh" }
-            python-version: "3.8"
+            python-version: "3.10"
           - platform:
               { name: "macos", os: "macos-latest", shell: "bash -l {0}" }
-            python-version: "3.9"
+            python-version: "3.12"  # MacOS can't run 3.12 yet...
           - platform: { name: "windows", os: "windows-latest", shell: "pwsh" }
-            python-version: "3.9"
+            python-version: "3.11"
     environment:
       name: sire-build
     defaults:
@@ -49,7 +49,7 @@ jobs:
       REPO: "${{ github.repository }}"
     steps:
       #
-      - uses: conda-incubator/setup-miniconda@v2
+      - uses: conda-incubator/setup-miniconda@v3
         with:
           auto-update-conda: true
           python-version: ${{ matrix.python-version }}
@@ -62,7 +62,7 @@ jobs:
         run: git clone https://github.com/${{ env.REPO }} -b ${{ github.event.inputs.branch }} sire
       #
       - name: Setup Conda
-        run: mamba install -y -c conda-forge boa anaconda-client packaging=21 pip-requirements-parser
+        run: mamba install -y -c conda-forge boa anaconda-client packaging pip-requirements-parser
       #
       - name: Update Conda recipe
         run: python ${{ github.workspace }}/sire/actions/update_recipe.py

.github/workflows/devel.yaml

@@ -15,10 +15,10 @@ jobs:
     name: build (${{ matrix.python-version }}, ${{ matrix.platform.name }})
     runs-on: ${{ matrix.platform.os }}
     strategy:
-      max-parallel: 5
+      max-parallel: 6
       fail-fast: false
       matrix:
-        python-version: ["3.9", "3.10", "3.11"]
+        python-version: ["3.10", "3.11", "3.12"]
         platform:
           - { name: "windows", os: "windows-latest", shell: "pwsh" }
           - { name: "linux", os: "ubuntu-latest", shell: "bash -l {0}" }
@@ -28,11 +28,11 @@ jobs:
           # but Linux
           - platform:
               { name: "macos", os: "macos-latest", shell: "bash -l {0}" }
-            python-version: "3.9"
-          - platform: { name: "windows", os: "windows-latest", shell: "pwsh" }
-            python-version: "3.9"
+            python-version: "3.12"  # MacOS can't run 3.12 yet... We want 3.10 and 3.11
           - platform: { name: "windows", os: "windows-latest", shell: "pwsh" }
             python-version: "3.10"
+          - platform: { name: "windows", os: "windows-latest", shell: "pwsh" }
+            python-version: "3.11"
     environment:
       name: sire-build
     defaults:
@@ -44,7 +44,7 @@ jobs:
       REPO: "${{ github.repository }}"
     steps:
       #
-      - uses: conda-incubator/setup-miniconda@v2
+      - uses: conda-incubator/setup-miniconda@v3
         with:
           auto-update-conda: true
           python-version: ${{ matrix.python-version }}
@@ -57,7 +57,7 @@ jobs:
         run: git clone https://github.com/${{ env.REPO }} sire
       #
       - name: Setup Conda
-        run: mamba install -y -c conda-forge boa anaconda-client packaging=21 pip-requirements-parser
+        run: mamba install -y -c conda-forge boa anaconda-client packaging pip-requirements-parser
       #
       - name: Update Conda recipe
         run: python ${{ github.workspace }}/sire/actions/update_recipe.py

.github/workflows/main.yaml

@@ -24,11 +24,15 @@ jobs:
       max-parallel: 9
       fail-fast: false
       matrix:
-        python-version: ["3.9", "3.10", "3.11"]
+        python-version: ["3.10", "3.11", "3.12"]
         platform:
           - { name: "windows", os: "windows-latest", shell: "pwsh" }
           - { name: "linux", os: "ubuntu-latest", shell: "bash -l {0}" }
           - { name: "macos", os: "macos-latest", shell: "bash -l {0}" }
+        exclude:
+          - platform:
+              { name: "macos", os: "macos-latest", shell: "bash -l {0}" }
+            python-version: "3.12"  # MacOS can't run 3.12 yet...
     environment:
       name: sire-build
     defaults:
@@ -40,7 +44,7 @@ jobs:
       REPO: "${{ github.event.pull_request.head.repo.full_name || github.repository }}"
     steps:
       #
-      - uses: conda-incubator/setup-miniconda@v2
+      - uses: conda-incubator/setup-miniconda@v3
         with:
           auto-update-conda: true
           python-version: ${{ matrix.python-version }}
@@ -53,7 +57,7 @@ jobs:
         run: git clone -b main https://github.com/openbiosim/sire sire
       #
       - name: Setup Conda
-        run: mamba install -y -c conda-forge boa anaconda-client packaging=21 pip-requirements-parser
+        run: mamba install -y -c conda-forge boa anaconda-client packaging pip-requirements-parser
       #
       - name: Update Conda recipe
         run: python ${{ github.workspace }}/sire/actions/update_recipe.py

.github/workflows/pr.yaml

@@ -17,7 +17,7 @@ jobs:
       max-parallel: 5
       fail-fast: false
       matrix:
-        python-version: ["3.9", "3.10", "3.11"]
+        python-version: ["3.10", "3.11", "3.12"]
         platform:
           - { name: "windows", os: "windows-latest", shell: "pwsh" }
           - { name: "linux", os: "ubuntu-latest", shell: "bash -l {0}" }
@@ -27,14 +27,14 @@ jobs:
           # but Linux
           - platform:
               { name: "macos", os: "macos-latest", shell: "bash -l {0}" }
-            python-version: "3.9"
+            python-version: "3.10"
           - platform: { name: "windows", os: "windows-latest", shell: "pwsh" }
-            python-version: "3.9"
+            python-version: "3.10"
           - platform:
               { name: "macos", os: "macos-latest", shell: "bash -l {0}" }
-            python-version: "3.10"
+            python-version: "3.12"  # MacOS can't run 3.12 yet...
           - platform: { name: "windows", os: "windows-latest", shell: "pwsh" }
-            python-version: "3.10"
+            python-version: "3.11"
     environment:
       name: sire-build
     defaults:
@@ -46,7 +46,7 @@ jobs:
       REPO: "${{ github.event.pull_request.head.repo.full_name || github.repository }}"
     steps:
       #
-      - uses: conda-incubator/setup-miniconda@v2
+      - uses: conda-incubator/setup-miniconda@v3
         with:
           auto-update-conda: true
           python-version: ${{ matrix.python-version }}
@@ -59,7 +59,7 @@ jobs:
         run: git clone -b ${{ github.head_ref }} --single-branch https://github.com/${{ env.REPO }} sire
       #
       - name: Setup Conda
-        run: mamba install -y -c conda-forge boa anaconda-client packaging=21 pip-requirements-parser
+        run: mamba install -y -c conda-forge boa anaconda-client packaging pip-requirements-parser
       #
       - name: Update Conda recipe
         run: python ${{ github.workspace }}/sire/actions/update_recipe.py

README.rst

@@ -43,18 +43,53 @@ To create a new environment:
 
 .. code-block:: bash
 
-    conda create -n openbiosim "python<3.12"
+    conda create -n openbiosim "python<3.13"
     conda activate openbiosim
     conda install -c conda-forge -c openbiosim sire
 
 To install the latest development version you can use:
 
 .. code-block:: bash
 
-    conda create -n openbiosim-dev "python<3.12"
+    conda create -n openbiosim-dev "python<3.13"
     conda activate openbiosim-dev
     conda install -c conda-forge -c openbiosim/label/dev sire
 
+Installing older versions
+-------------------------
+
+You can install a specific version of sire by specifying the version number
+in the conda install command, e.g.
+
+.. code-block:: bash
+
+    conda install -c conda-forge -c openbiosim sire==2024.1.0
+
+Note that limited space means that we can only keep a small number of
+versions of sire on the official openbiosim conda channel. Generally
+these are all point releases of the latest major version, plus the latest
+point release of the last major version.
+
+We do provide an
+`archive channel <https://openbiosim.blob.core.windows.net/archive/index.html>`__
+of all previous releases. You can search this archive channel for the
+release you are interested in using the following command:
+
+.. code-block:: bash
+
+    conda search -c https://openbiosim.blob.core.windows.net/archive sire
+
+This will return a list of all versions of sire available in the archive.
+
+You can install a specific version from the archive using a command like:
+
+.. code-block:: bash
+
+    conda install -c https://openbiosim.blob.core.windows.net/archive sire==2023.2.3
+
+Installation from source
+------------------------
+
 However, as you are here, it is likely you want to download the latest,
 greatest version of the code, which you will need to compile. To compile
 sire,

actions/update_recipe.py

@@ -254,4 +254,4 @@ def check_reqs(reqs0, reqs1):
 channels = " ".join([f"-c {x}" for x in channels])
 
 print("\nBuild this package using the command")
-print(f"conda mambabuild {channels} {condadir}")
+print(f"conda build {channels} {condadir}")

corelib/src/libs/SireBase/CMakeLists.txt

@@ -27,6 +27,7 @@ set ( SIREBASE_HEADERS
       combineproperties.h
       convert_property.hpp
       countflops.h
+      console.h
       cpuid.h
       errors.h
       findexe.h
@@ -87,6 +88,7 @@ set ( SIREBASE_SOURCES
       chunkedhash.cpp
       chunkedvector.cpp
       combineproperties.cpp
+      console.cpp
       countflops.cpp
       cpuid.cpp
       errors.cpp

corelib/src/libs/SireBase/console.cpp

@@ -0,0 +1,88 @@
+/********************************************\
+  *
+  *  Sire - Molecular Simulation Framework
+  *
+  *  Copyright (C) 2024  Christopher Woods
+  *
+  *  This program is free software; you can redistribute it and/or modify
+  *  it under the terms of the GNU General Public License as published by
+  *  the Free Software Foundation; either version 3 of the License, or
+  *  (at your option) any later version.
+  *
+  *  This program is distributed in the hope that it will be useful,
+  *  but WITHOUT ANY WARRANTY; without even the implied warranty of
+  *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+  *  GNU General Public License for more details.
+  *
+  *  You should have received a copy of the GNU General Public License
+  *  along with this program; if not, write to the Free Software
+  *  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
+  *
+  *  For full details of the license please see the COPYING file
+  *  that should have come with this distribution.
+  *
+  *  You can contact the authors via the website
+  *  at https://sire.openbiosim.org
+  *
+\*********************************************/
+
+#include "SireBase/console.h"
+
+using namespace SireBase;
+
+ConsoleBase::ConsoleBase()
+{
+}
+
+ConsoleBase::~ConsoleBase()
+{
+}
+
+ConsoleBase *Console::c(0);
+
+Console::Console()
+{
+}
+
+Console::~Console()
+{
+}
+
+/** Write the passed debug message to the console */
+void Console::debug(const QString &message)
+{
+    if (c)
+        c->debug(message);
+}
+
+/** Write the passed warning message to the console */
+void Console::warning(const QString &message)
+{
+    if (c)
+        c->warning(message);
+}
+
+/** Write the passed error message to the console */
+void Console::error(const QString &message)
+{
+    if (c)
+        c->error(message);
+}
+
+/** Write the passed info message to the console */
+void Console::info(const QString &message)
+{
+    if (c)
+        c->info(message);
+}
+
+/** Set the driver for the global console - this will delete
+ *  any existing console - and will take ownership of the pointer!
+ */
+void Console::setConsole(ConsoleBase *console)
+{
+    if (c)
+        delete c;
+
+    c = console;
+}