From 327f6825b8ccb32ad7b2a30e540ee9f57f882fe4 Mon Sep 17 00:00:00 2001
From: Jonathan Karr <jonrkarr@gmail.com>
Date: Mon, 20 Sep 2021 15:54:58 -0400
Subject: [PATCH] build: added polling for PySCeS release to PyPI, updated
 Dockerfile to install PySCeS from PyPI

---
 .github/workflows/ci.yml         | 41 +++++++++++++++++++++++---------
 .gitignore                       |  1 +
 Dockerfile                       | 20 ++++++++++++++--
 Dockerfile-base                  | 21 ----------------
 biosimulators_pysces/_version.py |  2 +-
 5 files changed, 50 insertions(+), 35 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 63cb047..ea80b3d 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -53,6 +53,16 @@ jobs:
       #############################################
       ## Update the version of the simulator
       #############################################
+      - name: Check that the version of the simulator is available from PyPI
+        if: github.event.inputs.simulatorVersion
+        uses: emilioschepis/wait-for-endpoint@v1.0.0
+        with:
+          url: https://pypi.org/pypi/pysces/${{ github.event.inputs.simulatorVersion }}/json
+          method: GET
+          expected-status: 200
+          timeout: 3600000 # 1 hr
+          interval: 60000 # 1 min
+
       - name: Update the version of the simulator
         if: github.event.inputs.simulatorVersion
         run: |
@@ -127,17 +137,26 @@ jobs:
           python -m pip install git+https://github.com/modelon-community/Assimulo.git@Assimulo-${ASSIMULO_VERSION}
 
       - name: Install PySCeS
-        env:
-          PYSCES_REVISION: 470cd0b8afa4c14721a2b2bc00d4c71d80603801
-        run: |
-          sudo apt-get update -y
-          sudo apt-get install -y --no-install-recommends \
-            git \
-            gcc \
-            gfortran \
-            libgfortran5
-          
-          python -m pip install git+https://github.com/PySCeS/pysces.git@${PYSCES_REVISION}
+        uses: nick-invision/retry@v2
+        with:
+          timeout_minutes: 20
+          retry_on: error
+          retry_wait_seconds: 300
+          max_attempts: 4
+          command: |
+            sudo apt-get update -y
+            sudo apt-get install -y --no-install-recommends jq
+
+            SIMULATOR_VERSION=$(jq -r '.version' biosimulators.json)
+
+            sudo apt-get update -y
+            sudo apt-get install -y --no-install-recommends \
+              git \
+              gcc \
+              gfortran \
+              libgfortran5
+                      
+            python -m pip install "pysces==${SIMULATOR_VERSION}"
 
       # install package
       - name: Install the package
diff --git a/.gitignore b/.gitignore
index 4eb7a01..e7d7f93 100644
--- a/.gitignore
+++ b/.gitignore
@@ -5,6 +5,7 @@ __pycache__/
 dist/
 build/
 _pystmptmp*_parsetab.py
+*-sbml_conversion_errors.txt
 
 # coverage files
 htmlcov/
diff --git a/Dockerfile b/Dockerfile
index eaf3b1c..777f51c 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -1,7 +1,7 @@
 # Base OS
 FROM ghcr.io/biosimulators/biosimulators_pysces/pysces_base:latest
 
-ARG VERSION=0.1.21
+ARG VERSION=0.1.22
 ARG SIMULATOR_VERSION="1.0.0"
 
 # metadata
@@ -29,6 +29,23 @@ LABEL \
     extra.identifiers.biotools="pysces" \
     maintainer="BioSimulators Team <info@biosimulators.org>"
 
+# install PySCeS
+RUN apt-get update -y \
+    && apt-get install -y --no-install-recommends \
+        git \
+        gcc \
+        gfortran \
+        libgfortran5 \
+    \
+    && pip install "pysces[all]==${SIMULATOR_VERSION}" \
+    \
+    && apt-get remove -y \
+        git \
+        gcc \
+        gfortran \
+    && apt-get autoremove -y \
+    && rm -rf /var/lib/apt/lists
+
 # Copy code for command-line interface into image and install it
 COPY . /root/Biosimulators_PySCeS
 RUN pip install /root/Biosimulators_PySCeS \
@@ -40,7 +57,6 @@ RUN pip install /root/Biosimulators_PySCeS \
     && cp /root/Biosimulators_PySCeS/.pys_usercfg.Dockerfile.ini /Pysces/.pys_usercfg.ini \
     && cp /root/Biosimulators_PySCeS/.pys_usercfg.Dockerfile.ini /root/Pysces/.pys_usercfg.ini \
     && rm -rf /root/Biosimulators_PySCeS
-RUN pip install "pysces==${SIMULATOR_VERSION}"
 
 # supported environment variables
 ENV ALGORITHM_SUBSTITUTION_POLICY=SIMILAR_VARIABLES \
diff --git a/Dockerfile-base b/Dockerfile-base
index 4ecb564..6f6cee8 100644
--- a/Dockerfile-base
+++ b/Dockerfile-base
@@ -54,27 +54,6 @@ RUN apt-get update -y \
     && apt-get autoremove -y \
     && rm -rf /var/lib/apt/lists
 
-# install Python requirements for PySCeS
-RUN pip install ipyparallel
-
-# install PySCeS
-ARG PYSCES_REVISION=7478a05bc4480e580fabfe89acb259274ced7f6c
-RUN apt-get update -y \
-    && apt-get install -y --no-install-recommends \
-        git \
-        gcc \
-        gfortran \
-        libgfortran5 \
-    \
-    && pip install git+https://github.com/PySCeS/pysces.git@${PYSCES_REVISION} \
-    \
-    && apt-get remove -y \
-        git \
-        gcc \
-        gfortran \
-    && apt-get autoremove -y \
-    && rm -rf /var/lib/apt/lists
-
 # fonts for matplotlib
 RUN apt-get update -y \
     && apt-get install -y --no-install-recommends libfreetype6 \
diff --git a/biosimulators_pysces/_version.py b/biosimulators_pysces/_version.py
index dccb61c..872472a 100644
--- a/biosimulators_pysces/_version.py
+++ b/biosimulators_pysces/_version.py
@@ -1 +1 @@
-__version__ = '0.1.21'
+__version__ = '0.1.22'