Merge branch 'main' into dev

.flake8

@@ -15,5 +15,6 @@
 # E741: ambiguous variable name 'l' (too pedantic! get a good font)
 # E711: sometimes needed for comparison to ROOT nullptr (better to cast to bool)
 # F401: unused import (some may have side effects, need to clean by hand)
-ignore = F403,F405,E402,W504,E203,W503,E262,E265,E266,E501,E741,E711,F401
+# E721: do not compare types (new, could be fixed relatively easily)
+ignore = F403,F405,E402,W504,E203,W503,E262,E265,E266,E501,E741,E711,F401,E721
 max-line-length = 160

.github/workflows/ci.yml

@@ -57,11 +57,17 @@ jobs:
     - name: Install build environment
       shell: bash -l {0}
       run: |
-        mamba install -c conda-forge python==${{ matrix.python }} pip pandas root==${{ matrix.root }} gsl tbb vdt boost pcre eigen
+        mamba install -c conda-forge python==${{ matrix.python }} pip pandas root==${{ matrix.root }} gsl tbb vdt boost-cpp boost pcre eigen
         cd HiggsAnalysis/CombinedLimit
         bash set_conda_env_vars.sh
     - name: Build
       shell: bash -l {0}
       run: |
         cd HiggsAnalysis/CombinedLimit
         make CONDA=1 -j 2
+    - name: Run tests
+      if: startsWith(matrix.python, '3.')
+      shell: bash -l {0}
+      run: |
+        cd HiggsAnalysis/CombinedLimit/test
+        python test_interference.py

Makefile

@@ -53,11 +53,12 @@ DICTNAME=$(LIBNAME)_xr
 # Linker and flags -------------------------------------------------------------
 LD = $(shell root-config --ld)
 ROOTLDFLAGS   = $(shell root-config --ldflags)
+ROOTLIBDIR = $(shell root-config --libdir)
 # OS x specific linkage
 DARWIN := $(shell uname|grep Darwin)
 ifdef DARWIN
-LDFLAGS       = $(ROOTLDFLAGS) -shared -install_name @rpath/$(SONAME) -fPIC
-EXELDFLAGS    = -Wl,-rpath,'@executable_path/../lib'
+LDFLAGS       = $(ROOTLDFLAGS) -g -shared -install_name @rpath/$(SONAME) -fPIC
+EXELDFLAGS    = -Wl,-rpath,'@executable_path/../lib' -Wl,-rpath,$(ROOTLIBDIR)
 else
 LDFLAGS       = $(ROOTLDFLAGS) -shared -Wl,-soname,$(SONAME) -Wl,-E -Wl,-z,defs -fPIC
 EXELDFLAGS    = 
@@ -97,7 +98,7 @@ $(OBJ_DIR):
 	@mkdir -p $(OBJ_DIR)/a
 
 $(OBJ_DIR)/a/$(DICTNAME).cc: $(SRC_DIR)/classes_def.xml | $(OBJ_DIR)
-	genreflex $(SRC_DIR)/classes.h -s $< -o $@ --deep --fail_on_warnings --rootmap=$(OBJ_DIR)/a/$(DICTNAME).rootmap --rootmap-lib=$(SONAME) -I$(PARENT_DIR)
+	genreflex $(SRC_DIR)/classes.h -s $< -o $@ --deep --fail_on_warnings --rootmap=$(OBJ_DIR)/a/$(DICTNAME).rootmap --rootmap-lib=$(SONAME) -Isrc -I$(PARENT_DIR)
 	mv $(OBJ_DIR)/a/$(DICTNAME).rootmap $(LIB_DIR)/
 	mv $(OBJ_DIR)/a/$(DICTNAME)_rdict.pcm $(LIB_DIR)/
 

bin/PerfTest.cpp

@@ -6,8 +6,8 @@
 #include "RooMsgService.h"
 #include <dlfcn.h>
 #include <RooStats/ModelConfig.h>
-#include "HiggsAnalysis/CombinedLimit/interface/CachingNLL.h"
-#include "HiggsAnalysis/CombinedLimit/interface/ProfilingTools.h"
+#include "../interface/CachingNLL.h"
+#include "../interface/ProfilingTools.h"
 
 void (*dump_)(const char *);
 

bin/combine.cpp

@@ -26,7 +26,7 @@
 #include "../interface/CascadeMinimizer.h"
 #include "../interface/ProfilingTools.h"
 #include "../interface/GenerateOnly.h"
-#include "../interface/Logger.h"
+#include "../interface/CombineLogger.h"
 #include <map>
 
 using namespace std;
@@ -51,6 +51,9 @@ int main(int argc, char **argv) {
 
   Combine combiner;
 
+  // Set name of Log file (ideally would make this similar format to out file)
+  CombineLogger::instance().setName("combine_logger.out");
+
   map<string, LimitAlgo *> methods;
   algo = new Significance(); methods.insert(make_pair(algo->name(), algo));
   algo = new BayesianFlatPrior(); methods.insert(make_pair(algo->name(), algo));
@@ -250,6 +253,7 @@ int main(int argc, char **argv) {
   }
 
   TString fileName = "higgsCombine" + name + "."+whichMethod+"."+massName+toyName+"root";
+
   TFile *test = new TFile(fileName, "RECREATE"); outputFile = test;
   TTree *t = new TTree("limit", "limit");
   int syst, iToy, iSeed, iChannel; 
@@ -324,7 +328,7 @@ int main(int argc, char **argv) {
 
   try {
      combiner.run(datacard, dataset, limit, limitErr, iToy, t, runToys);
-     if (verbose>0) Logger::instance().printLog(); 
+     if (verbose>0) CombineLogger::instance().printLog(); 
   } catch (std::exception &ex) {
      cerr << "Error when running the combination:\n\t" << ex.what() << std::endl;
      test->Close();

contributing.md

@@ -0,0 +1,119 @@
+# Contributing
+
+Contributions to combine of all sizes, from minor documentation updates to big code improvements, are welcome and encouraged.
+
+To ensure good development of the tool, we try to coordinate contributions.
+However, we are happy to help overcome any steps that may pose issues for contributors.
+
+Guidelines for contributions are below.
+
+In general you should always perform the following steps when contributing.
+
+1. Make your changes;
+2. Test your changes to ensure they work and don't break anything;
+3. If this changes any user-facing aspect, ensure that the appropriate documentation is updated;
+4. Check code style (see below), and fix any issues;
+5. Create your pull request;
+6. Iterate with the maintainers until the request is merged.
+
+## Code Style
+
+
+We ask that you put some effort into the readability of your code.
+We are, however, always happy to help if there is an issue.
+
+We use linting as part of our ci/cd for the python code. 
+That means your code will be checked automatically, and you must make sure it conforms to certain rules.
+
+Currently no linting or automatic checks of C++ code are implemented.
+Although we do not have a well-defined style guide for C++, we always appreciate readable and well-formatted code.
+
+### Technical details on linting
+
+we use `flake8` and `black` for linting. 
+To run the linting locally before making your pull request, or before making a commit, you can do the following.
+
+ensure `flake8` and `black` are installed: 
+
+```
+ python -m pip install -q flake8 black
+```
+
+and then from the main directory of this repository run
+
+
+flake8:
+```
+flake8 .
+```
+
+and black:
+
+```
+black -l 160 --check --diff .
+```
+
+If you'd like to see the details of the configuration `flake8` is using, check the `.flake8` file in the main directory.
+The black linting uses the default [black style](https://black.readthedocs.io/en/stable/the_black_code_style/current_style.html) (for v23.3.0), with only the command line options shown above.
+
+
+## Updating Documentation
+
+It is crucial to our user base and developers that the documentation is well-maintained.
+For that reason, whenever you make a change you should consider whether this requires a corresponding documentation update.
+
+If the change is user-facing it almost certainly does require a documentation update.
+
+Documentation is **very important** to us. 
+Therefore, we will be picky and make sure it is done well!
+However, we don't want to put extra burden on you, so we are happy to help and will make our own edits and updates to improve the documentation of your change.
+
+We appreciate you putting in some effort and thought to ensure:
+
+- your documentation is understandable to the audience being targeted;
+- your documentation is clear and concise; and
+- your documentation fits in properly with the overall documentation structure.
+
+### Technical details of the documentation
+
+We use [mkdocs](www.mkdocs.org) to produce the static website that documents combine.
+
+The documentation files are all under the `docs/` folder.
+Which pages get included in the site, and other configuration details are set in the `mkdocs.yml` file.
+
+In order to check the documentation rendering (features such as latex math rendering, etc) locally, you can generate the site on your local computer and check it in your browser.
+To do so, after [installing mkdocs](https://www.mkdocs.org/getting-started/) and [pymdown extensions](https://facelessuser.github.io/pymdown-extensions/installation/) and the [cinder theme](https://sourcefoundry.org/cinder/) via:
+
+```
+python -m pip install mkdocs pymdown-extensions mkdocs-cinder
+```
+
+ you can do:
+
+```
+mkdocs build
+mkdocs serve
+```
+
+from the main repository directory. mkdocs will then print a link you can open to check the page generated in your browser.
+
+**NOTE:** mkdocs builds which use internal links (or images etc) with absolute paths will work for local deployment, but will break when deployed to the public documentations pages. 
+Please ensure you use relative paths. Currently, this is the only known feature where the behvaiour differs between local mkdocs and public pages deployment. 
+If you'd like to test the deployment directly, the suggested method is to set up a docs page using your personal github account; this should mimic the exact settings of the official page.
+
+## Big Contributions
+
+We welcome large contributions to combine. 
+Note, however, that we also follow long term planning, and there is a dedicated group stewarding the overall direction and development of the code.
+
+This means that the code development should fit in with our long term vision;
+if you have an idea for a big improvement or change it will be most efficient if you [contact us](mailto:[email protected]) first, in order to ensure that we can integrate it as seemlessly as possible into our plans.
+This will simplify any potential conflicts when you make your pull request.
+
+## Requested Contributions
+
+As part of the long term planning, we have a number of changes we are targeting, but have not yet had a chance to implement.
+As well as the [issues](https://github.com/cms-analysis/HiggsAnalysis-CombinedLimit/issues) listed on the github issues tracker, you can see the [projects](https://github.com/orgs/cms-analysis/projects) listed under the general cms-analysis organization, where we have defined several projects and areas we are targeting.
+If you're interested in getting involved in any of these projects please contact us at [[email protected]](mailto:[email protected]).
+
+