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Get tgen working on all shadow-supported platforms #20

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Dec 10, 2021
Merged

Get tgen working on all shadow-supported platforms #20

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2616cf2
Test on platforms supported by shadow
sporksmith Dec 8, 2021
fc52b53
Replace usage of private igraph_i_attribute_gettype
sporksmith Dec 8, 2021
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134 changes: 130 additions & 4 deletions .github/workflows/ci.yml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -2,6 +2,11 @@
# https://help.github.com/en/actions/automating-your-workflow-with-github-actions/workflow-syntax-for-github-actions

name: Tests
permissions: read-all

defaults:
run:
shell: bash

on:
push:
Expand All @@ -13,36 +18,157 @@ on:
- '**.md'
- 'LICENSE'

env:
DEBIAN_FRONTEND: noninteractive

jobs:
testing:
runs-on: ubuntu-latest
container:
image: ${{ matrix.container }}
strategy:
matrix:
cc: ['gcc', 'clang']
container:
- 'ubuntu:18.04'
- 'ubuntu:20.04'
- 'debian:10-slim'
- 'debian:11-slim'
- 'fedora:34'
- 'quay.io/centos/centos:stream8'
steps:
- name: Update packages
run: sudo apt-get update
run: |
case ${{ matrix.container }} in
ubuntu* | debian*)
apt-get update
;;
esac

- name: Checkout
uses: actions/checkout@v2

- name: Install tgen dependencies
run: sudo apt-get install -y ${{ matrix.cc }} cmake libglib2.0-0 libglib2.0-dev libigraph0v5 libigraph0-dev
run: |
case ${{ matrix.container }} in
ubuntu*)
apt-get install -y \
${{ matrix.cc }} \
cmake \
libglib2.0-0 \
libglib2.0-dev \
libigraph0v5 \
libigraph0-dev
;;
debian*)
apt-get install -y \
${{ matrix.cc }} \
cmake \
libglib2.0-0 \
libglib2.0-dev \
libigraph-dev
;;
fedora*)
dnf install -y \
${{ matrix.cc }} \
cmake \
glib2 \
glib2-devel \
igraph \
igraph-devel
;;
*centos*stream8)
dnf install -y \
${{ matrix.cc }} \
cmake \
glib2 \
glib2-devel
dnf install -y https://dl.fedoraproject.org/pub/archive/epel/7.7/x86_64/Packages/i/igraph-0.7.1-12.el7.x86_64.rpm
dnf install -y https://dl.fedoraproject.org/pub/archive/epel/7.7/x86_64/Packages/i/igraph-devel-0.7.1-12.el7.x86_64.rpm
;;
*)
echo "Unhandled container ${{ matrix.container }}"
exit 1
esac

- name: Build tgen
run: mkdir -p build && cd build && CC=${{ matrix.cc }} cmake .. && make

- name: Install test dependencies
run: |
case ${{ matrix.container }} in
fedora* | *centos*)
dnf install -y \
diffutils
;;
esac

- name: Test mmodel
run: bash test/run_mmodel_tests.sh

- name: Test tgen
run: bash test/run_tgen_integration_tests.sh

- name: Install tgentools dependencies
run: sudo apt install -y python3 python3-dev python3-pip python3-venv libxml2 libxml2-dev libxslt1.1 libxslt1-dev libpng16-16 libpng-dev libfreetype6 libfreetype6-dev libblas-dev liblapack-dev
run: |
case ${{ matrix.container }} in
ubuntu* | debian*)
apt install -y \
gfortran \
python3 \
python3-dev \
python3-pip \
python3-venv \
libjpeg-dev \
libxml2 \
libxml2-dev \
libxslt1.1 \
libxslt1-dev \
libpng16-16 \
libpng-dev \
libfreetype6 \
libfreetype6-dev \
libblas-dev \
liblapack-dev
;;
fedora*)
dnf install -y \
cmake \
glib2 \
glib2-devel \
libdeflate \
python3 \
python3-pip \
xz
pip3 install virtualenv
;;
*centos*)
dnf install -y \
cmake \
glib2 \
glib2-devel \
libjpeg-turbo \
libjpeg-turbo-devel \
platform-python-devel \
python3 \
python3-pip \
xz \
zlib \
zlib-devel

pip3 install virtualenv
;;
*)
echo "Unhandled container ${{ matrix.container }}"
exit 1
esac

- name: Build tgentools
run: python3 -m venv build/toolsenv && source build/toolsenv/bin/activate && pip3 install -r tools/requirements.txt && pip3 install -I tools/
run: |
python3 -m venv build/toolsenv
source build/toolsenv/bin/activate
pip3 install -r tools/requirements.txt
pip3 install -I tools/

- name: Test tgentools
run: bash test/run_tgentools_integration_tests.sh
91 changes: 57 additions & 34 deletions src/tgen-markovmodel.c
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -92,6 +92,36 @@ struct _TGenMarkovModel {
guint magic;
};

// igraph_i_attribute_gettype was removed from igraph in 0.9. The closest
// replacement appears to be `igraph_cattribute_table.gettype`, though it's
// unclear from the documentation whether it's guaranteed to be non-NULL nor
// whether it's intended to be callable by users of the library.
//
// Therefore we make a best-effort to detect type mismatches, but may not
// always be able to do so.
static gboolean tgenmarkovmodel_attributeTypeMismatch(const igraph_t *graph, igraph_attribute_type_t desiredType,
igraph_attribute_elemtype_t elemtype, const char *name) {
if (!igraph_cattribute_table.gettype) {
// We don't know whether there's a type mismatch. No harm done if the
// types are correct, but potentially surprising behavior if they're
// not.
tgen_warning("Internal error: igraph_cattribute_table.gettype missing; unable to validate attribute types");
return FALSE;
}
igraph_attribute_type_t type = IGRAPH_ATTRIBUTE_DEFAULT;
if (igraph_cattribute_table.gettype(graph, &type, elemtype, name) != IGRAPH_SUCCESS) {
// The igraph documentation says it'll abort on any error, but in case
// it doesn't, error out here.
tgen_warning("igraph_cattribute_table.gettype failed; unable to validate attribute type");
return TRUE;
}
if (type != desiredType) {
tgen_warning("got type %d instead of %d for attribute '%s'", type, desiredType, name);
return TRUE;
}
return FALSE;
}

static const gchar* _tgenmarkovmodel_vertexAttributeToString(VertexAttribute attr) {
if(attr == VERTEX_ATTR_ID) {
return "name";
Expand Down Expand Up @@ -226,7 +256,7 @@ static gboolean _tgenmarkovmodel_vertexIDIsEmission(const gchar* idStr) {
}
}

/* if the value is found and not NULL, it's value is returned in valueOut.
/* if the value is found and not NULL, its value is returned in valueOut.
* returns true if valueOut has been set, false otherwise */
static gboolean _tgenmarkovmodel_findVertexAttributeString(TGenMarkovModel* mmodel, igraph_integer_t vertexIndex,
VertexAttribute attr, const gchar** valueOut) {
Expand All @@ -239,24 +269,22 @@ static gboolean _tgenmarkovmodel_findVertexAttributeString(TGenMarkovModel* mmod
const gchar* name = _tgenmarkovmodel_vertexAttributeToString(attr);

if(igraph_cattribute_has_attr(mmodel->graph, IGRAPH_ATTRIBUTE_VERTEX, name)) {
igraph_attribute_type_t type = IGRAPH_ATTRIBUTE_DEFAULT;
igraph_i_attribute_gettype(mmodel->graph, &type, IGRAPH_ATTRIBUTE_VERTEX, name);

if(type == IGRAPH_ATTRIBUTE_STRING) {
const gchar* value = igraph_cattribute_VAS(mmodel->graph, name, vertexIndex);
if(value != NULL && value[0] != '\0') {
if(valueOut != NULL) {
*valueOut = value;
return TRUE;
}
if (tgenmarkovmodel_attributeTypeMismatch(mmodel->graph, IGRAPH_ATTRIBUTE_STRING, IGRAPH_ATTRIBUTE_VERTEX, name)) {
return FALSE;
}
const gchar* value = igraph_cattribute_VAS(mmodel->graph, name, vertexIndex);
if(value != NULL && value[0] != '\0') {
if(valueOut != NULL) {
*valueOut = value;
return TRUE;
}
}
}

return FALSE;
}

/* if the value is found and not NULL, it's value is returned in valueOut.
/* if the value is found and not NULL, its value is returned in valueOut.
* returns true if valueOut has been set, false otherwise */
static gboolean _tgenmarkovmodel_findEdgeAttributeDouble(TGenMarkovModel* mmodel, igraph_integer_t edgeIndex,
EdgeAttribute attr, gdouble* valueOut) {
Expand All @@ -265,25 +293,22 @@ static gboolean _tgenmarkovmodel_findEdgeAttributeDouble(TGenMarkovModel* mmodel
const gchar* name = _tgenmarkovmodel_edgeAttributeToString(attr);

if(igraph_cattribute_has_attr(mmodel->graph, IGRAPH_ATTRIBUTE_EDGE, name)) {
igraph_attribute_type_t type = IGRAPH_ATTRIBUTE_DEFAULT;
igraph_i_attribute_gettype(mmodel->graph, &type, IGRAPH_ATTRIBUTE_EDGE, name);

if(type == IGRAPH_ATTRIBUTE_NUMERIC) {
gdouble value = (gdouble) igraph_cattribute_EAN(mmodel->graph, name, edgeIndex);
if(isnan(value) == 0) {
if(valueOut != NULL) {
*valueOut = value;
return TRUE;
}
if (tgenmarkovmodel_attributeTypeMismatch(mmodel->graph, IGRAPH_ATTRIBUTE_NUMERIC, IGRAPH_ATTRIBUTE_EDGE, name)) {
return FALSE;
}
gdouble value = (gdouble) igraph_cattribute_EAN(mmodel->graph, name, edgeIndex);
if(isnan(value) == 0) {
if(valueOut != NULL) {
*valueOut = value;
return TRUE;
}
}

}

return FALSE;
}

/* if the value is found and not NULL, it's value is returned in valueOut.
/* if the value is found and not NULL, its value is returned in valueOut.
* returns true if valueOut has been set, false otherwise */
static gboolean _tgenmarkovmodel_findEdgeAttributeString(TGenMarkovModel* mmodel, igraph_integer_t edgeIndex,
EdgeAttribute attr, const gchar** valueOut) {
Expand All @@ -296,16 +321,14 @@ static gboolean _tgenmarkovmodel_findEdgeAttributeString(TGenMarkovModel* mmodel
const gchar* name = _tgenmarkovmodel_edgeAttributeToString(attr);

if(igraph_cattribute_has_attr(mmodel->graph, IGRAPH_ATTRIBUTE_EDGE, name)) {
igraph_attribute_type_t type = IGRAPH_ATTRIBUTE_DEFAULT;
igraph_i_attribute_gettype(mmodel->graph, &type, IGRAPH_ATTRIBUTE_EDGE, name);

if(type == IGRAPH_ATTRIBUTE_STRING) {
const gchar* value = igraph_cattribute_EAS(mmodel->graph, name, edgeIndex);
if(value != NULL && value[0] != '\0') {
if(valueOut != NULL) {
*valueOut = value;
return TRUE;
}
if (tgenmarkovmodel_attributeTypeMismatch(mmodel->graph, IGRAPH_ATTRIBUTE_STRING, IGRAPH_ATTRIBUTE_EDGE, name)) {
return FALSE;
}
const gchar* value = igraph_cattribute_EAS(mmodel->graph, name, edgeIndex);
if(value != NULL && value[0] != '\0') {
if(valueOut != NULL) {
*valueOut = value;
return TRUE;
}
}
}
Expand Down