900: bumped pybind11 version and added setuptools on host (#1050)

* bumped pybind11 version and added setuptools on host * updated pybind11 tarball to 2.13 and in cmakefile to get 2.13 frpm github, also updated documentation about pybind 2.13 * update release notes, doc * updating readme --------- Co-authored-by: Erik Fröjdh <[email protected]>
slsdetectorgroup · Nov 22, 2024 · 7ea6b31 · 7ea6b31
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commit 7ea6b31
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diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -309,14 +309,15 @@ if (SLS_USE_PYTHON)
         FetchContent_Declare(
             pybind11
             GIT_REPOSITORY https://github.com/pybind/pybind11
-            GIT_TAG        v2.11.0
+            GIT_TAG        v2.13.0
         )
 
     else()
+    # https://github.com/pybind/pybind11/releases
         FetchContent_Declare(
             pybind11
-            URL ${CMAKE_SOURCE_DIR}/libs/pybind11/v2.11.0.tar.gz
-            URL_HASH MD5=90c4946e87c64d8d8fc0ae4edf35d780
+            URL ${CMAKE_SOURCE_DIR}/libs/pybind11/v2.13.0.tar.gz
+            URL_HASH MD5=10cb1efba3aca997389d08bceb0ea767
         )
     endif()
     FetchContent_MakeAvailable(pybind11)

diff --git a/README.md b/README.md
@@ -2,7 +2,11 @@
 Before building from source make sure that you have the [software wiki](https://slsdetectorgroup.github.io/devdoc/dependencies.html) installed. If installing using conda, conda will manage the dependencies. Avoid also installing packages with pip. 
 
 ## Documentaion
-Detailed documentation can be found in the [software wiki](https://slsdetectorgroup.github.io/devdoc/index.html) and on the [official site](https://www.psi.ch/en/detectors/software).
+Detailed documentation including installation can be found in the [software wiki](https://slsdetectorgroup.github.io/devdoc/index.html).
+
+Different releases can be found on the [official site](https://www.psi.ch/en/lxn/software-releases).
+
+Firmware compatiblity can be found in [firmware page](https://github.com/slsdetectorgroup/slsDetectorFirmware)
 
 ## Installation
 
@@ -42,33 +46,20 @@ conda search slsdet
 conda search slsdetgui
 ```
 
-### 2. Build from source
+## 2. Build from source
 
-##### 2.1 Download Source Code from github
+### 2.1 Download Source Code from github
 ```
 git clone https://github.com/slsdetectorgroup/slsDetectorPackage.git --branch 7.0.0
 ```
 
-**Pybind for Python**<br>
-* **v7.0.0+**:
-pybind11 packaged into 'libs/pybind'. No longer a submodule. No need for "recursive" or "submodule update".
-
-* **Older versions**:
-   pybind11 is a submodule. Must be cloned using "recursive" and updated when switching between versions using the following commands.
-
-```
-# clone using recursive to get pybind11 submodule
-git clone --recursive https://github.com/slsdetectorgroup/slsDetectorPackage.git
+> **Note:** For v6.x.x of slsDetectorPackage and older, refer [pybind11 notes on cloning](#Pybind-and-Zeromq).
 
-# update submodule when switching between releases
-cd slsDetectorPackage
-git submodule update --init
-```
 
-##### 2.2 Build from source
+### 2.2 Build from source
 
 
-###### Build using CMake
+### Build using CMake
 
 ```
 # outside slsDetecorPackage folder
@@ -94,26 +85,28 @@ Instead of the cmake command, one can use ccmake to get a list of options to con
 ccmake ..
  
 # choose the options
-# first press [c] - configure
+# first press [c] - configure (unil you see [g])
 # then press [g] - generate
 ```
 
 |Example cmake options|Comment|
 |---|---|
 | -DSLS_USE_PYTHON=ON            | Python                                 |   
-| -DPython_FIND_VIRTUALENV=ONLY  | Python from only the conda environment |
-| -DZeroMQ_HINT=/usr/lib64       | Use system zmq instead                 |    
+| -DPython_FIND_VIRTUALENV=ONLY  | Python from only the conda env         | 
 | -DSLS_USE_GUI=ON               | GUI                                    |
+| -DSLS_USE_HDF5=ON              | HDF5                                   |
+| -DSLS_USE_SIMULATOR=ON         | Simulator                              |
 
+> **Note:** For v7.x.x of slsDetectorPackage and older, refer [zeromq notes for cmake option to hint library location](#Pybind-and-Zeromq).
 
-###### Build using in-built cmk.sh script
+### Build using in-built cmk.sh script
 
 ```
 The binaries are generated in slsDetectorPackage/build/bin directory.
 
-Usage: ./cmk.sh [-b] [-c] [-d <HDF5 directory>] [e] [g] [-h] [i] [-j <Number of threads>] 
-[-k <CMake command>] [-l <Install directory>] [m] [n] [-p] [-q <Zmq hint directory>] 
-[r] [s] [t] [u] [z]  
+Usage: $0 [-b] [-c] [-d <HDF5 directory>] [-e] [-g] [-h] [-i]
+[-j <Number of threads>] [-k <CMake command>] [-l <Install directory>]
+[-m] [-n] [-p] [-r] [-s] [-t] [-u] [-z]
 -[no option]: only make
 -b: Builds/Rebuilds CMake files normal mode
 -c: Clean
@@ -128,14 +121,13 @@ Usage: ./cmk.sh [-b] [-c] [-d <HDF5 directory>] [e] [g] [-h] [i] [-j <Number of
 -m: Manuals
 -n: Manuals without compiling doxygen (only rst)
 -p: Builds/Rebuilds Python API
--q: Zmq hint directory
 -r: Build/Rebuilds only receiver
 -s: Simulator
 -t: Build/Rebuilds only text client
 -u: Chip Test Gui
 -z: Moench zmq processor
 
-    
+
 # display all options
 ./cmk.sh -?
 
@@ -145,11 +137,14 @@ Usage: ./cmk.sh [-b] [-c] [-d <HDF5 directory>] [e] [g] [-h] [i] [-j <Number of
 # new build, python and compile in parallel:
 ./cmk.sh -cbpj5
 
-#To use the system zmq (/usr/lib64) instead
-./cmk.sh -cbj5 -q /usr/lib64
+#For rebuilding only certain sections
+./cmk.sh -tg #only text client and gui
+./cmk.sh -r #only receiver
 ```
 
-###### Build on old distributions
+> **Note:** For v7.x.x of slsDetectorPackage and older, refer [zeromq notes for cmk script option to hint library location](#Pybind-and-Zeromq).
+
+### Build on old distributions
 
 If your linux distribution doesn't come with a C++11 compiler (gcc>4.8) then 
 it's possible to install a newer gcc using conda and build the slsDetectorPackage
@@ -166,7 +161,10 @@ cmake ../slsDetectorPackage -DCMAKE_PREFIX_PATH=$CONDA_PREFIX
 make -j12
 ```
 
-###### Build slsDetectorGui (Qt5)
+> **Note:** For v7.x.x of slsDetectorPackage and older, refer [zeromq notes for dependencies for conda](#Pybind-and-Zeromq).
+
+
+### Build slsDetectorGui (Qt5)
 
 1. Using pre-built binary on conda
 ```
@@ -180,7 +178,14 @@ yum install qt5-qtbase-devel.x86_64
 yum install qt5-qtsvg-devel.x86_64 
 ```
 
-3. Using conda
+3. Using system installation on RHEL8
+```
+yum install qt5-qtbase-devel.x86_64
+yum install qt5-qtsvg-devel.x86_64 
+yum install expat-devel.x86_64
+```
+
+4. Using conda
 ```
 #Add channels for dependencies and our library
 conda config --add channels conda-forge
@@ -208,13 +213,15 @@ cd slsDetectorPackage
 ./cmk.sh -cbgj9
 ```
 
-###### Build documentation from package
+> **Note:** For v7.x.x of slsDetectorPackage and older, refer [zeromq notes for dependencies for conda](#Pybind-and-Zeromq).
+
+### Build documentation from package
 The documentation for the slsDetectorPackage is build using a combination 
 of Doxygen, Sphinx and Breathe. The easiest way to install the dependencies
 is to use conda 
 
 ```
-conda create -n myenv python sphinx_rtd_theme breathe
+conda create -n myenv python=3.12 sphinx sphinx_rtd_theme breathe doxygen numpy
 ```
 
 ```
@@ -228,6 +235,47 @@ make rst # rst only, saves time in case the API did not change
 ```
 
 
+
+## Pybind and Zeromq
+
+### Pybind11 for Python
+**v8.0.0+**:
+pybind11 is built
+* by default from tar file in repo (libs/pybind/v2.1x.0.tar.gz)
+* or use advanced option SLS_FETCH_PYBIND11_FROM_GITHUB [link].
+   * v9.0.0+: pybind11 (v2.13.0)
+   * v8.x.x : pybind11 (v2.11.0)
+
+**v7.x.x**:
+pybind11 packaged into ‘libs/pybind’. No longer a submodule. No need for “recursive” or “submodule update”.
+
+**Older versions**:
+pybind11 is a submodule. Must be cloned using “recursive” and updated when switching between versions using the following commands.
+
+```
+# Note: Only for v6.x.x versions and older
+
+# clone using recursive to get pybind11 submodule
+git clone --recursive https://github.com/slsdetectorgroup/slsDetectorPackage.git
+
+# update submodule when switching between releases
+cd slsDetectorPackage
+git submodule update --init
+```
+
+### Zeromq
+**v8.0.0+**:
+zeromq (v4.3.4) is built
+* by default from tar file in repo (libs/libzmq/libzmq-4.3.4.tar.gz)
+* or use advanced option SLS_FETCH_ZMQ_FROM_GITHUB [link].
+
+**v7.x.x and older**:
+zeromq-devel must be installed and one can hint its location using
+* cmake option:’-DZeroMQ_HINT=/usr/lib64’ or
+* option ‘-q’ in cmk.sh script: : ./cmk.sh -cbj5 -q /usr/lib64
+* ‘zeromq’ dependency added when installing using conda
+
+
 ## Support
     [email protected]
-    [email protected]
+    [email protected]
diff --git a/RELEASE.txt b/RELEASE.txt
@@ -1,4 +1,4 @@
-SLS Detector Package Major Release 3.0.0 released on 31.10.2024
+SLS Detector Package Major Release 9.0.0 released on 22.11.2024
 ===============================================================
 
 This document describes the differences between v9.0.0 and v8.0.2
@@ -24,13 +24,20 @@ This document describes the differences between v9.0.0 and v8.0.2
 =====================
 
 
+    *   Pybind11 version
+        In-built version and the one picked up from github 
+        updated from v2.11 to v2.13
+
+
     *   Python version
         slsdet.__version__ now returns the package release version.
 
+
     *   Python build in Conda
         Added python 3.13 also to conda build
 
 
+
 2 New, Changed or Resolved Features
 =====================================
 
@@ -304,7 +311,7 @@ This document describes the differences between v9.0.0 and v8.0.2
 
     Gotthard2   03.10.2024 (v1.0)                   (updated in 9.0.0)
 
-    Moench      26.10.2023 (v2.0)                   (updated in 9.0.0)
+    Moench      26.10.2023 (v2.0)                   (updated in 8.0.2)
 
     Gotthard    08.02.2018 (50um and 25um Master)
                 09.02.2018 (25 um Slave) 

diff --git a/conda-recipe/meta.yaml b/conda-recipe/meta.yaml
@@ -79,12 +79,13 @@ outputs:
         - {{compiler('cxx')}}
         - {{ pin_subpackage('slsdetlib', exact=True) }}
         - setuptools
-        - pybind11=2.11
+        - pybind11=2.13
 
       host:
         - python
         - {{ pin_subpackage('slsdetlib', exact=True) }}
-        - pybind11=2.11
+        - setuptools
+        - pybind11=2.13
 
 
       run:

diff --git a/docs/src/dependencies.rst b/docs/src/dependencies.rst
@@ -21,7 +21,7 @@ Python bindings
 -----------------------
 
  * Python > 3.6
- * pybind11 2.11.0 (packaged in libs)
+ * pybind11 2.13.0 (packaged in libs)
 
 .. note ::  
 

diff --git a/docs/src/installation.rst b/docs/src/installation.rst
@@ -103,7 +103,7 @@ Instead of the cmake command, one can use ccmake to get a list of options to con
     ccmake ..
  
     # choose the options
-    # first press [c] - configure (maybe multiple times till you see [g])
+    # first press [c] - configure (until you see [g])
     # then press [g] - generate
 
 
@@ -287,11 +287,13 @@ Pybind and Zeromq
 .. _pybind for different slsDetectorPackage versions:
 
 
-| **Pybind for Python**
-| v8.0.0+:
-|   pybind11 (v2.11.0) is built 
-|   * by default from tar file in repo (libs/pybind/v2.11.0.tar.gz) 
+| **Pybind11 for Python**
+| v8.0.0+: 
+|   pybind11 is built
+|   * by default from tar file in repo (libs/pybind/v2.1x.0.tar.gz) 
 |   * or use advanced option SLS_FETCH_PYBIND11_FROM_GITHUB [`link <https://github.com/pybind/pybind11>`__].
+|      * v9.0.0+: pybind11 (v2.13.0)
+|      * v8.x.x : pybind11 (v2.11.0)
 |
 | v7.x.x:
 |   pybind11 packaged into 'libs/pybind'. No longer a submodule. No need for "recursive" or "submodule update".

diff --git a/libs/pybind11/v2.11.0.tar.gz b/libs/pybind11/v2.11.0.tar.gz
diff --git a/libs/pybind11/v2.13.0.tar.gz b/libs/pybind11/v2.13.0.tar.gz
diff --git a/slsSupportLib/include/sls/versionAPI.h b/slsSupportLib/include/sls/versionAPI.h
@@ -1,8 +1,6 @@
 // SPDX-License-Identifier: LGPL-3.0-or-other
 // Copyright (C) 2021 Contributors to the SLS Detector Package
 /** API versions */
-#define APIRECEIVER  "9.0.0 0x241014"
-#define APILIB       "9.0.0 0x241018"
 #define APICTB       "9.0.0 0x241121"
 #define APIGOTTHARD  "9.0.0 0x241121"
 #define APIGOTTHARD2 "9.0.0 0x241121"
@@ -11,3 +9,5 @@
 #define APIXILINXCTB "9.0.0 0x241121"
 #define APIEIGER     "9.0.0 0x241121"
 #define APIMYTHEN3   "9.0.0 0x241121"
+#define APILIB       "developer 0x241122"
+#define APIRECEIVER  "developer 0x241122"