1370-1 Move function definitions from .cpp to header for upcoming templatization by julianlitz · Pull Request #1374 · SciCompMod/memilio

julianlitz · 2025-09-15T14:11:30Z

Changes and Information

Please briefly list the changes (main added features, changed items, or corrected bugs) made:

Moved IO functions from source to header file, such that they can be templated

If need be, add additional information and what the reviewer should look out for in particular:

Nothing in the implementation has changed
Forward declaration of in .cpp remaining functions
Lay foundation to resolve issue Add support for reading templated SECIR models from JSON data #1370

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julianlitz · 2025-09-16T08:41:18Z

cpp/memilio/io/mobility_io.cpp

-#include "memilio/math/eigen.h"
-#include "memilio/utils/logging.h"
-
-#ifdef MEMILIO_HAS_HDF5
-#include "memilio/io/hdf5_cpp.h"
-#endif // MEMILIO_HAS_HDF5
-
-#include <iostream>
-#include <fstream>
-#include <string>
-#include <vector>


Includes are now needed in header instead.

julianlitz · 2025-09-16T08:41:48Z

cpp/memilio/io/mobility_io.h

 * @param filename name of file to be read
 */
-IOResult<Eigen::MatrixXd> read_mobility_formatted(const std::string& filename);
+template <typename FP = ScalarType>


Add a dummy template to be able to move it to the header without conflicts.

julianlitz · 2025-09-16T08:42:15Z

cpp/memilio/io/mobility_io.h

 IOResult<void> save_edges(const std::vector<std::vector<TimeSeries<ScalarType>>>& ensemble_edges,
                          const std::vector<std::pair<int, int>>& pairs_edges, const fs::path& result_dir,
-                          bool save_single_runs = true, bool save_percentiles = true);
+                          bool save_single_runs = true, bool save_percentiles = true)


Ensure keeping default setting
bool save_percentiles = true

julianlitz · 2025-09-16T08:43:16Z

cpp/models/ode_secir/parameters_io.h

+// Forward declaration of get_region_id
+int get_region_id(int id);


Add forward declaration for in .cpp remaining functions.

julianlitz · 2025-09-16T08:43:53Z

cpp/models/ode_secirvvs/parameters_io.h

 IOResult<void> read_confirmed_cases_data(
-    std::string const& path, std::vector<int> const& vregion, Date date, std::vector<std::vector<double>>& num_Exposed,
-    std::vector<std::vector<double>>& num_InfectedNoSymptoms, std::vector<std::vector<double>>& num_InfectedSymptoms,
-    std::vector<std::vector<double>>& num_InfectedSevere, std::vector<std::vector<double>>& num_icu,
-    std::vector<std::vector<double>>& num_death, std::vector<std::vector<double>>& num_rec,
-    const std::vector<std::vector<int>>& t_Exposed, const std::vector<std::vector<int>>& t_InfectedNoSymptoms,
-    const std::vector<std::vector<int>>& t_InfectedSymptoms, const std::vector<std::vector<int>>& t_InfectedSevere,
-    const std::vector<std::vector<int>>& t_InfectedCritical, const std::vector<std::vector<double>>& mu_C_R,
-    const std::vector<std::vector<double>>& mu_I_H, const std::vector<std::vector<double>>& mu_H_U,
-    const std::vector<double>& scaling_factor_inf);
+    const std::vector<ConfirmedCasesDataEntry>& rki_data, std::vector<int> const& vregion, Date date,


Swapped two function declarations here.

Define A first.
Then define B which uses A.

julianlitz · 2025-09-16T08:44:22Z

cpp/models/ode_secirvvs/parameters_io.h

 IOResult<void> read_confirmed_cases_data_fix_recovered(const std::vector<ConfirmedCasesDataEntry>& rki_data,
                                                       std::vector<int> const& vregion, Date date,
-                                                       std::vector<std::vector<double>>& vnum_rec, double delay = 14.);
+                                                       std::vector<std::vector<double>>& vnum_rec, double delay = 14.0)


Ensure keeping default parameter
double delay = 14.0

julianlitz · 2025-09-16T08:45:13Z

pycode/memilio-simulation/memilio/simulation/bindings/models/osecir.cpp

+                                              decltype(mio::read_mobility_plain<double>)>(
+                mobility_data_file, params_graph, mobile_comp, contact_locations_size, mio::read_mobility_plain<double>,
+                weights);


Pycode explicitly needs these double template parameters.

julianlitz · 2025-09-16T08:46:25Z

cpp/memilio/io/result_io.h

+template <typename FP = ScalarType>
+IOResult<void> save_result(const std::vector<TimeSeries<ScalarType>>& results, const std::vector<int>& ids,
+                           int num_groups, const std::string& filename)


Be careful if names are different in .h and .cpp.
Here result -> results differs.

julianlitz added 4 commits September 15, 2025 12:27

Move from source to header

6557812

I like to move it move it

e9c2cbc

Pycode templates

24ec698

mio::read_mobility_plain<double>

71833e4

julianlitz commented Sep 16, 2025

View reviewed changes

julianlitz self-assigned this Sep 16, 2025

julianlitz added loc::backend This issue concerns the C++ backend implementation. class::improvement Cleanup that doesn't affect functionality labels Sep 16, 2025

julianlitz mentioned this pull request Sep 16, 2025

1370-2 Add support for reading templated SECIR models from JSON data #1375

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julianlitz requested review from MaxBetzDLR and reneSchm September 16, 2025 09:39

MaxBetzDLR added this to MEmilio: Equation-Based-Models Development Oct 9, 2025

MaxBetzDLR moved this to 👀 Review in MEmilio: Equation-Based-Models Development Oct 9, 2025

mknaranja moved this from 👀 Review to On hold in MEmilio: Equation-Based-Models Development Nov 20, 2025

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1370-1 Move function definitions from .cpp to header for upcoming templatization#1374

1370-1 Move function definitions from .cpp to header for upcoming templatization#1374
julianlitz wants to merge 4 commits intomainfrom
1370-move-source-to-header

julianlitz commented Sep 15, 2025 •

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		// Forward declaration of get_region_id
		int get_region_id(int id);

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julianlitz commented Sep 15, 2025 •

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