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Yaml implementation #125

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merged 4 commits into from
Dec 10, 2023
Merged

Yaml implementation #125

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661fe5c
First version of from_yaml and to_yaml serialization. Updated minimum…
vitenti Dec 9, 2023
7220119
Complete version of the yaml serialization, including special types.
vitenti Dec 10, 2023
f1eb657
Updated Python stubs.
vitenti Dec 10, 2023
59f1afb
Adding fyaml to CI.
vitenti Dec 10, 2023
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6 changes: 3 additions & 3 deletions .github/workflows/build_check.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -19,7 +19,7 @@ jobs:
- name: Install pre-requisites
run: |
sudo apt-get update
sudo apt-get install gobject-introspection gir1.2-glib-2.0 libgirepository1.0-dev gcc gfortran pkg-config libglib2.0-dev libgmp3-dev libmpfr-dev libgsl0-dev libfftw3-dev libopenblas-dev libflint-arb-dev libcfitsio-dev libnlopt-dev libhdf5-dev gtk-doc-tools texlive texlive-bibtex-extra texlive-science texlive-publishers tex4ht perl libxml-libxml-perl
sudo apt-get install gobject-introspection gir1.2-glib-2.0 libgirepository1.0-dev gcc gfortran pkg-config libglib2.0-dev libgmp3-dev libmpfr-dev libgsl0-dev libfftw3-dev libopenblas-dev libflint-arb-dev libcfitsio-dev libfyaml-dev libnlopt-dev libhdf5-dev gtk-doc-tools texlive texlive-bibtex-extra texlive-science texlive-publishers tex4ht perl libxml-libxml-perl
sudo pip install meson ninja pytest numpy
- name: Ensure clear Jupyter Notebooks
uses: ResearchSoftwareActions/EnsureCleanNotebooksAction@1.1
Expand Down Expand Up @@ -68,7 +68,7 @@ jobs:
- name: Install pre-requisites
run: |
sudo apt-get update
sudo apt-get install gobject-introspection gir1.2-glib-2.0 libgirepository1.0-dev gcc gfortran gcovr pkg-config libglib2.0-dev libgmp3-dev libmpfr-dev libgsl0-dev libfftw3-dev libopenblas-dev libflint-arb-dev libcfitsio-dev libnlopt-dev libhdf5-dev python3-setuptools gtk-doc-tools
sudo apt-get install gobject-introspection gir1.2-glib-2.0 libgirepository1.0-dev gcc gfortran gcovr pkg-config libglib2.0-dev libgmp3-dev libmpfr-dev libgsl0-dev libfftw3-dev libopenblas-dev libflint-arb-dev libcfitsio-dev libfyaml-dev libnlopt-dev libhdf5-dev python3-setuptools gtk-doc-tools
pip install meson ninja pytest numpy
- name: Configure NumCosmo
run: meson setup build -Ddebug=true -Db_coverage=true -Db_lto=false --prefix=/usr || (cat build/meson-logs/meson-log.txt && exit 1)
Expand Down Expand Up @@ -107,7 +107,7 @@ jobs:
python-version: '3.x'
- name: Brew install pre-requisites
run: |
brew install gobject-introspection gsl gmp mpfr fftw cfitsio nlopt gfortran gtk-doc glib openblas
brew install gobject-introspection gsl gmp mpfr fftw cfitsio libfyaml nlopt gfortran gtk-doc glib openblas
- name: Pip install pre-requisites
run: |
pip3 install meson ninja pytest numpy pygobject
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17 changes: 15 additions & 2 deletions meson.build
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Expand Up @@ -348,8 +348,7 @@ dl_dep = dependency('dl', method: 'auto')
# Dependencies versions:
#######################################################################################

glib_req = '>= 2.44.0'
gobject_req = '>= 2.44.0'
glib_req = '>= 2.54.0'
gsl_req = '>= 2.4'
fftw_req = '>= 3.1.2'
cfitsio_req = '>= 3.25'
Expand Down Expand Up @@ -498,6 +497,20 @@ if cfitsio_dep.found()
numcosmo_conf.set('HAVE_CFITSIO', true)
endif

#######################################################################################
# Checking for libfyaml
#######################################################################################
message('Checking for libfyaml')

libfyaml_dep = dependency(
'libfyaml',
required: false,
)

if libfyaml_dep.found()
numcosmo_conf.set('HAVE_LIBFYAML', true)
endif

#######################################################################################
# Using internal libcuba:
#######################################################################################
Expand Down
31 changes: 0 additions & 31 deletions numcosmo/data/nc_data_reduced_shear_cluster_mass.c
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Expand Up @@ -657,37 +657,6 @@ ncm_hdf5_table_free (NcmHDF5Table *h5tb)
g_free (h5tb);
}

#if !GLIB_CHECK_VERSION (2, 54, 0)

static gboolean
g_ptr_array_find_with_equal_func (GPtrArray *haystack,
gconstpointer needle,
GEqualFunc equal_func,
guint *index_)
{
guint i;

g_return_val_if_fail (haystack != NULL, FALSE);

if (equal_func == NULL)
equal_func = g_direct_equal;

for (i = 0; i < haystack->len; i++)
{
if (equal_func (g_ptr_array_index (haystack, i), needle))
{
if (index_ != NULL)
*index_ = i;

return TRUE;
}
}

return FALSE;
}

#endif

gboolean
ncm_hdf5_table_has_col (NcmHDF5Table *h5tb, const gchar *col)
{
Expand Down
15 changes: 5 additions & 10 deletions numcosmo/math/ncm_cfg.c
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Expand Up @@ -493,10 +493,6 @@ ncm_cfg_init_full_ptr (gint *argc, gchar ***argv)
fftwf_set_timelimit (10.0);
#endif /* HAVE_FFTW3F */

#if !GLIB_CHECK_VERSION (2, 36, 0)
g_type_init ();
#endif

_log_stream = stdout;
_log_stream_err = stderr;

Expand Down Expand Up @@ -1067,14 +1063,13 @@ static guint nreg_model = 0;
void
ncm_cfg_register_obj (GType obj)
{
#if GLIB_CHECK_VERSION (2, 34, 0)
g_type_ensure (obj);
{
gpointer obj_class = g_type_class_ref (obj);

#endif /* GLIB >= 2.34*/
gpointer obj_class = g_type_class_ref (obj);

g_type_class_unref (obj_class);
nreg_model++;
g_type_class_unref (obj_class);
nreg_model++;
}
}

/**
Expand Down
2 changes: 1 addition & 1 deletion numcosmo/math/ncm_matrix.c
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Expand Up @@ -169,7 +169,7 @@ ncm_matrix_class_init (NcmMatrixClass *klass)
*/
g_object_class_install_property (object_class, PROP_VALS,
g_param_spec_variant ("values", NULL, "values",
G_VARIANT_TYPE_ARRAY, NULL,
G_VARIANT_TYPE ("aad"), NULL,
G_PARAM_READWRITE | G_PARAM_STATIC_NAME | G_PARAM_STATIC_BLURB));
}

Expand Down
31 changes: 0 additions & 31 deletions numcosmo/math/ncm_mset_catalog.c
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Expand Up @@ -2560,37 +2560,6 @@ ncm_mset_catalog_col_symb (NcmMSetCatalog *mcat, guint i)
return ncm_mset_fparam_symbol (self->mset, i - self->nadd_vals);
}

#if !GLIB_CHECK_VERSION (2, 54, 0)

static gboolean
g_ptr_array_find_with_equal_func (GPtrArray *haystack,
gconstpointer needle,
GEqualFunc equal_func,
guint *index_)
{
guint i;

g_return_val_if_fail (haystack != NULL, FALSE);

if (equal_func == NULL)
equal_func = g_direct_equal;

for (i = 0; i < haystack->len; i++)
{
if (equal_func (g_ptr_array_index (haystack, i), needle))
{
if (index_ != NULL)
*index_ = i;

return TRUE;
}
}

return FALSE;
}

#endif

/**
* ncm_mset_catalog_col_by_name:
* @mcat: a #NcmMSetCatalog
Expand Down