Merge pull request #108 from smirarab/tippremove

4.5.0: Remove TIPP
smirarab · Feb 18, 2021 · bb54df5 · bb54df5
2 parents 4f3db01 + 2cfbe79
commit bb54df5
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Showing 14 changed files with 12 additions and 2,301 deletions.
diff --git a/.travis.yml b/.travis.yml
@@ -32,6 +32,6 @@ install:
 script:
   - COVERAGE_FILE=.coverage coverage run -p --concurrency=multiprocessing --rcfile .coveragerc setup.py nosetests -w test/unittest/
   - coverage combine
-  - flake8 run_tipp.py setup.py run_abundance.py split_sequences.py run_tipp_tool.py distribute_setup.py run_ensemble.py run_sepp.py run_upp.py merge_script.py test/unittest/ sepp/
+  - flake8  setup.py  split_sequences.py distribute_setup.py run_ensemble.py run_sepp.py run_upp.py merge_script.py test/unittest/ sepp/
 after_success:
   - coveralls
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,3 +1,5 @@
+* Version 4.5.0:
+    * TIPP has moved to a new repo: https://github.com/TeraTrees/TIPP
 * Version 4.4.0:
     * TIPP has moved to TIPP2
 * Version 4.3.21:

diff --git a/README.TIPP.md b/README.TIPP.md
diff --git a/README.md b/README.md
@@ -9,15 +9,15 @@ Each of these related tools has its own README file.
 [README.SEPP.md](README.SEPP.md)
 * **SEPP** stands for "SATe-enabled Phylogenetic Placement", and addresses the problem of phylogenetic placement of short reads into reference alignments and trees.
 
-[README.TIPP.md](README.TIPP.md)
-* **TIPP** stands for "Taxonomic Identification and Phylogenetic Profiling", and addresses the problem of taxonomic identification and abundance profiling of metagenomic data.
-
 [README.UPP.md](README.UPP.md)
 * **UPP** stands for "Ultra-large alignments using Phylogeny-aware Profiles", and addresses the problem of alignment of very large datasets, potentially containing fragmentary data. UPP can align datasets with up to 1,000,000 sequences.
 
 [README.HIPPI.md](README.HIPPI.md)
 * **HIPPI** stands for "Highly Accurate Protein Family Classification with Ensembles of HMMs", and addresses the problem of classifying query sequences to protein families.
 
+[README.TIPP.md](https://github.com/TeraTrees/TIPP/)
+* **TIPP** stands for "Taxonomic Identification and Phylogenetic Profiling", and addresses the problem of taxonomic identification and abundance profiling of metagenomic data. We have moved TIPP as a separate package from SEPP. TIPP package can be accessed [here](https://github.com/TeraTrees/TIPP/).
+
 ---------------------------------------------
 Bugs and Errors
 ---------------------------------------------

diff --git a/run_abundance.py b/run_abundance.py
diff --git a/run_tipp.py b/run_tipp.py
diff --git a/run_tipp_tool.py b/run_tipp_tool.py
diff --git a/sepp/__init__.py b/sepp/__init__.py
@@ -23,11 +23,11 @@
 
 __all__ = ['algorithm', 'alignment', 'backtranslate',
            'checkpointing', 'config', 'decompose_tree', 'ensemble',
-           'exhaustive', 'exhaustive_tipp', 'exhaustive_upp', 'filemgr',
-           'jobs', 'math_utils', 'metagenomics', 'problem', 'scheduler',
+           'exhaustive', 'exhaustive_upp', 'filemgr',
+           'jobs', 'math_utils', 'problem', 'scheduler',
            'scratch', 'tree', 'get_logger', 'is_temp_kept', 'version']
 
-version = "4.4.0"
+version = "4.5.0"
 _DEBUG = ("SEPP_DEBUG" in os.environ) and \
     (os.environ["SEPP_DEBUG"].lower() == "true")