fix: missing link in docs / libsbml (#455)

- missing link to notebook - use own python-libsbml index to get mac wheels
opencobra · Mar 13, 2017 · 88607f3 · 88607f3
1 parent 1b9aca1
commit 88607f3
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Showing 5 changed files with 22 additions and 30 deletions.
diff --git a/.travis.yml b/.travis.yml
@@ -69,7 +69,7 @@ matrix:
 before_install:
   - if [[ -n "${MB_PYTHON_VERSION}" ]]; then
       (travis_retry git clone https://github.com/matthew-brett/multibuild.git && cd multibuild && git checkout e6ebbfa);
-      TEST_DEPENDS="swiglpk optlang sympy decorator cython codecov coverage numpy scipy python-libsbml jsonschema six pytest pytest-cov pytest-benchmark tabulate";
+      TEST_DEPENDS="swiglpk optlang sympy decorator cython codecov coverage numpy scipy jsonschema six pytest pytest-cov pytest-benchmark tabulate";
       BUILD_DEPENDS="swiglpk optlang sympy cython numpy scipy";
       source multibuild/common_utils.sh;
       source multibuild/travis_steps.sh;

diff --git a/config.sh b/config.sh
@@ -56,5 +56,6 @@ function run_tests_in_repo {
 
 function run_tests {
     # Runs tests on installed distribution from an empty directory
+    pip install python-libsbml==5.12.1 -f https://s3.eu-central-1.amazonaws.com/moonlight-science/wheelhouse/index.html --no-cache-dir
     run_tests_in_repo
 }
diff --git a/documentation_builder/autodoc.sh b/documentation_builder/autodoc.sh
@@ -1,5 +1,5 @@
 rm cobra.rst cobra.*.rst
-sphinx-apidoc -o . ../cobra ../cobra/external \
-    ../cobra/test ../cobra/solvers/ ../cobra/test_all.py \
-    ../cobra/version.py ../cobra/solvers/legacy.py
+sphinx-apidoc -o . ../cobra \
+    ../cobra/test ../cobra/solvers/ \
+    ../cobra/solvers/legacy.py
 rm modules.rst
diff --git a/documentation_builder/getting_started.ipynb b/documentation_builder/getting_started.ipynb
@@ -38,16 +38,7 @@
     "deletable": true,
     "editable": true
    },
-   "outputs": [
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "/home/moritz/.virtualenvs/cobra/lib/python3.5/site-packages/optlang/gurobi_interface.py:26: UserWarning: Be careful! The GUROBI interface is still under construction ...\n",
-      "  warn(\"Be careful! The GUROBI interface is still under construction ...\")\n"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "from __future__ import print_function\n",
     "\n",
@@ -116,7 +107,7 @@
     {
      "data": {
       "text/plain": [
-       "<Reaction EX_glu__L_e at 0x7fbba1140208>"
+       "<Reaction EX_glu__L_e at 0x10eff01d0>"
       ]
      },
      "execution_count": 3,
@@ -150,7 +141,7 @@
     {
      "data": {
       "text/plain": [
-       "<Metabolite atp_c at 0x7fbba11730b8>"
+       "<Metabolite atp_c at 0x10efa52b0>"
       ]
      },
      "execution_count": 4,
@@ -228,7 +219,7 @@
     {
      "data": {
       "text/plain": [
-       "<Reaction PGI at 0x7fbba11568d0>"
+       "<Reaction PGI at 0x10f306828>"
       ]
      },
      "execution_count": 6,
@@ -557,7 +548,7 @@
     {
      "data": {
       "text/plain": [
-       "<Metabolite atp_c at 0x7fbba11730b8>"
+       "<Metabolite atp_c at 0x10efa52b0>"
       ]
      },
      "execution_count": 16,
@@ -724,10 +715,10 @@
     {
      "data": {
       "text/plain": [
-       "frozenset({<Reaction Biomass_Ecoli_core at 0x7fbba113c438>,\n",
-       "           <Reaction G6PDH2r at 0x7fbba1148ac8>,\n",
-       "           <Reaction GLCpts at 0x7fbba1148dd8>,\n",
-       "           <Reaction PGI at 0x7fbba11568d0>})"
+       "frozenset({<Reaction G6PDH2r at 0x10eff8a20>,\n",
+       "           <Reaction Biomass_Ecoli_core at 0x10efea2b0>,\n",
+       "           <Reaction GLCpts at 0x10eff8d30>,\n",
+       "           <Reaction PGI at 0x10f306828>})"
       ]
      },
      "execution_count": 21,
@@ -808,7 +799,7 @@
     {
      "data": {
       "text/plain": [
-       "frozenset({<Gene b4025 at 0x7fbba112ca90>})"
+       "frozenset({<Gene b4025 at 0x10efdc9b0>})"
       ]
      },
      "execution_count": 23,
@@ -832,7 +823,7 @@
     {
      "data": {
       "text/plain": [
-       "<Gene b4025 at 0x7fbba112ca90>"
+       "<Gene b4025 at 0x10efdc9b0>"
       ]
      },
      "execution_count": 24,
@@ -867,7 +858,7 @@
     {
      "data": {
       "text/plain": [
-       "frozenset({<Reaction PGI at 0x7fbba11568d0>})"
+       "frozenset({<Reaction PGI at 0x10f306828>})"
       ]
      },
      "execution_count": 25,
@@ -901,7 +892,7 @@
     {
      "data": {
       "text/plain": [
-       "frozenset({<Gene spam at 0x7fbba11321d0>, <Gene eggs at 0x7fbba1132cf8>})"
+       "frozenset({<Gene spam at 0x10efea748>, <Gene eggs at 0x10efea0f0>})"
       ]
      },
      "execution_count": 26,
@@ -960,7 +951,7 @@
     {
      "data": {
       "text/plain": [
-       "<Gene spam at 0x7fbba11321d0>"
+       "<Gene spam at 0x10efea748>"
       ]
      },
      "execution_count": 28,
@@ -1226,7 +1217,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.5.2+"
+   "version": "3.5.2"
   }
  },
  "nbformat": 4,

diff --git a/documentation_builder/index.rst b/documentation_builder/index.rst
@@ -19,8 +19,8 @@ be viewed at `nbviewer
     phenotype_phase_plane
     sampling
     loopless
-	solvers
-	constraints-objectives
+    solvers
+    constraints_objectives
     pymatbridge
     faq
     cobra