DOC: Update examples

README.md

@@ -90,20 +90,28 @@ internal_channel: http://${FSLCONDA_USERNAME}:${FSLCONDA_PASSWORD}@https://fsl.f
 
 # The FSL installation is created in two stages.
 # First of all, the base_packages are installed.
+# Versions of these packages are specified in
+# the packages list below
 base_packages:
- - fsl-base 2109.1
- - fsl-sub 2.5.8
- - fslpy 3.7.0
- - libopenblas 0.3.18 *openmp*
+ - fsl-base
+ - fslpy
+ - fsl-sub
+ - libopenblas
  ...
 
-# Then all of these packages are installed
-# in the second stage.
+# List of all packages that comprise a FSL
+# installation. All packages not installed
+# in the first stage (see base_packages
+# above) are installed in the second stage.
 packages:
  - ciftilib 1.5.3
  - fsleyes 1.3.0
+ - fslpy 3.7.0
  - fsl-avwutils 2007.0
+ - fsl-base 2109.1
  - fsl-eddy-cpu 2106.0
+ - fsl-sub 2.5.8
+ - libopenblas 0.3.18 *openmp*
  ...
 ```
 

manifest.example.json

@@ -60,6 +60,8 @@
         //                     builds.
         //   - "environment"   Conda environment.yml file
         //   - "sha256"        SHA256 checksum of environment.yml file
+        //   - "base_packages" List of "base" packages, which are
+        //                     installed before all other packages.
         //   - "output"        Dictionary containing number of lines of
         //                     output to expect when installing the FSL
         //                     environment ("install" : "100"), or when
@@ -71,6 +73,7 @@
                 "platform"      : "linux-64",
                 "environment"   : "https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/releases/fsl-6.1.0-linux-64.yml",
                 "sha256"        : "952a0101fc19948e785572f8c06436c59f19c4ef92df9425f2e2033d4b986918",
+                "base_packages" : ["fsl-base", "libopenblas", "fslpy"],
                 "output"        : {
                     "install"   : "92",
                     "6.0.6"     : "11"
@@ -80,6 +83,7 @@
                 "platform"      : "macos-64",
                 "environment"   : "https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/releases/fsl-6.1.0-macos-64.yml",
                 "sha256"        : "952a0101fc19948e785572f8c06436c59f19c4ef92df9425f2e2033d4b986918",
+                "base_packages" : ["fsl-base", "libopenblas", "fslpy"],
                 "output"        : {
                     "install"   : "92",
                     "6.0.6"     : "11"
@@ -90,6 +94,7 @@
                 "cuda"          : "9.2",
                 "environment"   : "https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/releases/fsl-6.1.0-linux-64-cuda9.2.yml",
                 "sha256"        : "952a0101fc19948e785572f8c06436c59f19c4ef92df9425f2e2033d4b986918",
+                "base_packages" : ["fsl-base", "libopenblas", "fslpy"],
                 "output"        : {
                     "install"   : "92",
                     "6.0.6"     : "11"
@@ -100,6 +105,7 @@
                 "cuda"          : "10.2",
                 "environment"   : "https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/releases/fsl-6.1.0-linux-64-cuda10.2.yml",
                 "sha256"        : "85ef650586c1d7f3475fe7d16108bb94b737decbfc7506ad4deff2917365d05f",
+                "base_packages" : ["fsl-base", "libopenblas", "fslpy"],
                 "output"        : {
                     "install"   : "92",
                     "6.0.6"     : "11"
@@ -111,6 +117,7 @@
                 "platform"      : "linux-64",
                 "environment"   : "https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/releases/fsl-6.2.0-linux-64.yml",
                 "sha256"        : "952a0101fc19948e785572f8c06436c59f19c4ef92df9425f2e2033d4b986918",
+                "base_packages" : ["fsl-base", "libopenblas", "fslpy"],
                 "output"        : {
                     "install"   : "92",
                     "6.0.6"     : "11",
@@ -121,6 +128,7 @@
                 "platform"      : "macos-64",
                 "environment"   : "https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/releases/fsl-6.2.0-macos-64.yml",
                 "sha256"        : "952a0101fc19948e785572f8c06436c59f19c4ef92df9425f2e2033d4b986918",
+                "base_packages" : ["fsl-base", "libopenblas", "fslpy"],
                 "output"        : {
                     "install"   : "92",
                     "6.0.6"     : "11",
@@ -132,6 +140,7 @@
                 "cuda"          : "9.2",
                 "environment"   : "https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/releases/fsl-6.2.0-linux-64-cuda9.2.yml",
                 "sha256"        : "952a0101fc19948e785572f8c06436c59f19c4ef92df9425f2e2033d4b986918",
+                "base_packages" : ["fsl-base", "libopenblas", "fslpy"],
                 "output"        : {
                     "install"   : "92",
                     "6.0.6"     : "11",
@@ -143,6 +152,7 @@
                 "cuda"          : "10.2",
                 "environment"   : "https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/releases/fsl-6.2.0-linux-64-cuda10.2.yml",
                 "sha256"        : "6499385a2f5d2da48f4a44c95e090a5156319b0acbbd47029d4270abc691a290",
+                "base_packages" : ["fsl-base", "libopenblas", "fslpy"],
                 "output"        : {
                     "install"   : "92",
                     "6.0.6"     : "11",