Remove matlab #3183
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Remove matlab #3183
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In preparation of upcoming work on the serialization, this commit adds a new testng option to the Bio-Formats automated tests allowing to define a directory for saving cache (memo) files. If configured, this cache directory can be later reused via a new dedicated FormatReaderTest.
Also adds testMemoFileUsage to a new "memoizer" group so that it can be run separately if needed.
If testng.cacheDirectory is set, then both the current and cached memo files will be tested. Otherwise, only the current memo file is tested.
gen-file-list requires testng.directory, testng.configDirectory, and testng.file-list to be set; the latter is the path to which the list will be written. See https://trello.com/c/x2nmObSk/191-bfmemo-change-detection
This allows test-automated to use a file listing created by gen-file-list, instead of scanning a directory. Using test-automated in this way now looks like: ant -Dtestng.configDirectory=/path/to/config -Dtestng.file-list=/path/to/file/list test-automated
Fixes warning reported by Findbugs.
The data file name stored in the header is not updated if the header and data files are renamed. If the stored data file name does not exist, then a file whose name is similar to the header file's name will be used (if such a file is present).
Image files can only be detected if a corresponding .hdr file exists, which won't work if either file was renamed.
Conflicts: components/formats-gpl/src/loci/formats/in/CellomicsReader.java
Repository: openmicroscopy/bioformats Already up-to-date. Generated by BIOFORMATS-DEV-latest-version-bump#73 (https://ci.openmicroscopy.org/job/BIOFORMATS-DEV-latest-version-bump/73/)
Update POM version numbers to 5.9.0-SNAPSHOT
switch modifier order to "static final" in readers
Remove Java 7 from Appveyor matrix
Fix download URLs in bf.bat and bf.sh
Clarify ordering expectation in get*UsedFiles Javadocs
OIR - Prevent infinite loop
This reverts commit ba7e58e.
Metamorph: override getDomains() to check if the current file has a plate
Plugins exporter: Reorder the dimensions
Volocity: expand Image names to include the stack parent name(s)
Inveon: attempt to find renamed data files
OBF: add basic FLIM support
Leica LIF: only prioritize C in dimension order if channels are RGB
Build updates
Warn if passing metadata with dimensionOrder in bfsave
MetaMorph - Prevent NullPointerException
FileStitcher: do not use detected patterns that include missing files
Initial version of Memoizer tests
Repository: openmicroscopy/bioformats Already up-to-date. Generated by BIOFORMATS-DEV-latest-version-bump#74 (https://ci.openmicroscopy.org/job/BIOFORMATS-DEV-latest-version-bump/74/)
Update the ImageJ API link for Javadoc crosslinks
Update POM version numbers to 5.9.0
Tag version 5.9.0
This is now decoupled in this repository: https://github.com/ome/bio-formats-matlab
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Closing as per #3444 (comment). |
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Rebase of #3135
Rebased onto sbesson/5.10.0-SNAPSHOT to avoid conflicts before #3180 is merged
This is now decoupled in this repository:
https://github.com/ome/bio-formats-matlab
Testing: Ensure that the travis and appveyor builds remain green.
CI changes:
dist-matlabanddist-octavetargets in these jobs: