From 601a78ce1121751a601b1096b1114c125dab08ea Mon Sep 17 00:00:00 2001
From: Chris Black <chris@ckblack.org>
Date: Fri, 9 Sep 2022 20:02:00 -0700
Subject: [PATCH 1/4] settings option is mandatory now

---
 DEV-INTRO.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/DEV-INTRO.md b/DEV-INTRO.md
index 0f399eff09e..de163841b83 100644
--- a/DEV-INTRO.md
+++ b/DEV-INTRO.md
@@ -245,7 +245,7 @@ You can submit your workflow either in the executor container or in rstudio cont
 docker-compose exec executor bash
 # inside the container
 cd /pecan/tests
-R CMD ../web/workflow.R docker.sipnet.xml
+R CMD ../web/workflow.R --settings docker.sipnet.xml
 ```
 
 A better way of doing this is developed as part of GSOC, in which case you can leverage of the restful interface defined, or using the new R PEcAn API package.

From 166dd299d03e71ea68e29101105c8595546adb66 Mon Sep 17 00:00:00 2001
From: Chris Black <chris@ckblack.org>
Date: Wed, 14 Sep 2022 13:29:13 -0700
Subject: [PATCH 2/4] clean before installing base

---
 docker/base/Dockerfile | 8 +++++++-
 1 file changed, 7 insertions(+), 1 deletion(-)

diff --git a/docker/base/Dockerfile b/docker/base/Dockerfile
index 2d1a624086e..7544497ddef 100644
--- a/docker/base/Dockerfile
+++ b/docker/base/Dockerfile
@@ -23,7 +23,13 @@ COPY base     /pecan/base/
 COPY modules  /pecan/modules/
 COPY models   /pecan/models/
 
-RUN cd /pecan && make && rm -rf /tmp/downloaded_packages
+# install all PEcAn packages
+# `make clean` is to remove artifacts copied in from host system
+#   (e.g. basgra.so)
+RUN cd /pecan \
+    && make clean \
+    && make \
+    && rm -rf /tmp/downloaded_packages
 
 # COPY WORKFLOW
 WORKDIR /work

From 75849147fbcc428f5d9b78019880b36ef3dcffdd Mon Sep 17 00:00:00 2001
From: Chris Black <chris@ckblack.org>
Date: Sat, 17 Sep 2022 22:26:58 -0700
Subject: [PATCH 3/4] missing word

---
 DEV-INTRO.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/DEV-INTRO.md b/DEV-INTRO.md
index de163841b83..f865c36c2cc 100644
--- a/DEV-INTRO.md
+++ b/DEV-INTRO.md
@@ -310,7 +310,7 @@ If you want to reset the pecan lib folder that is mounted across all machines, f
 
 ```
 docker-compose down
-docker rm pecan_lib
+docker volume rm pecan_lib
 ```
 
 ## Linux and User permissions

From c9c9a6c37645f123a9b0f8e754466993afa5547a Mon Sep 17 00:00:00 2001
From: Chris Black <chris@ckblack.org>
Date: Sat, 17 Sep 2022 22:27:48 -0700
Subject: [PATCH 4/4] service was renamed?

---
 docker-compose.dev.yml            | 2 +-
 docker/docker-compose.example.yml | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/docker-compose.dev.yml b/docker-compose.dev.yml
index c554492bc00..0eed697467e 100644
--- a/docker-compose.dev.yml
+++ b/docker-compose.dev.yml
@@ -8,7 +8,7 @@ services:
 
   # web application. This expects the config.php to be copied from docker/web
   # cp docker/web/config.docker.php web/config.php
-  #web:
+  #pecan:
   #  volumes:
   #    - 'pecan_web:/var/www/html/pecan'
 
diff --git a/docker/docker-compose.example.yml b/docker/docker-compose.example.yml
index 27ceea7d852..fd649f7bc93 100644
--- a/docker/docker-compose.example.yml
+++ b/docker/docker-compose.example.yml
@@ -7,7 +7,7 @@ services:
 
   # mount PEcAn web folder into web server, this allows for
   # editing code in PHP and immediatly test the new code.
-  web:
+  pecan:
     volumes:
       - ${HOME}/git/pecan/web:/var/www/html/pecan
       - ${HOME}/git/pecan/docker/config.docker.php:/var/www/html/pecan/config.php