diff --git a/CHANGES.txt b/CHANGES.txt index 90d45f9..843ede7 100644 --- a/CHANGES.txt +++ b/CHANGES.txt @@ -1,3 +1,7 @@ +3.1.24 + Update documentation + Fix tests + Remove dependency on python3-future 3.1.23: Use pytest instead of nose 3.1.21: diff --git a/README.md b/README.md index 4b73227..4cceeb2 100644 --- a/README.md +++ b/README.md @@ -110,7 +110,7 @@ From source: After dependencies installation, go in BioMAJ source directory: - python setup.py install + pip install . From packages: diff --git a/setup.py b/setup.py index 7da581a..398a8bf 100644 --- a/setup.py +++ b/setup.py @@ -36,7 +36,7 @@ def run(self): 'url': 'http://biomaj.genouest.org', 'download_url': 'http://biomaj.genouest.org', 'author_email': 'olivier.sallou@irisa.fr', - 'version': '3.1.23', + 'version': '3.1.24', 'classifiers': [ # How mature is this project? Common values are # 3 - Alpha diff --git a/tests/biomaj_tests.py b/tests/biomaj_tests.py index 6498f07..b56b3ec 100644 --- a/tests/biomaj_tests.py +++ b/tests/biomaj_tests.py @@ -77,7 +77,7 @@ def clean(self): def __copy_test_bank_properties(self): if self.bank_properties is not None: return - self.bank_properties = ['alu', 'local', 'testhttp','directhttp', + self.bank_properties = ['pdbaa', 'local', 'testhttp','directhttp', 'alu_list_error'] curdir = os.path.dirname(os.path.realpath(__file__)) for b in self.bank_properties: @@ -146,10 +146,10 @@ def setup_method(self, m): BiomajConfig.load_config(self.utils.global_properties, allow_user_config=False) # Delete all banks - b = Bank('alu') + b = Bank('pdbaa') b.banks.remove({}) - self.config = BiomajConfig('alu') + self.config = BiomajConfig('pdbaa') data_dir = self.config.get('data.dir') lock_file = os.path.join(data_dir,'alu.lock') if os.path.exists(lock_file): @@ -166,13 +166,13 @@ def test_new_bank(self): """ Checks bank init """ - b = Bank('alu') + b = Bank('pdbaa') def test_new_session(self): """ Checks an empty session is created """ - b = Bank('alu') + b = Bank('pdbaa') b.load_session(UpdateWorkflow.FLOW) for key in b.session._session['status'].keys(): assert not(b.session.get_status(key)) @@ -181,14 +181,14 @@ def test_session_reload_notover(self): """ Checks a session is used if present """ - b = Bank('alu') + b = Bank('pdbaa') for i in range(1, 5): - s = Session('alu', self.config, UpdateWorkflow.FLOW) + s = Session('pdbaa', self.config, UpdateWorkflow.FLOW) s._session['status'][Workflow.FLOW_INIT] = True b.session = s b.save_session() - b = Bank('alu') + b = Bank('pdbaa') b.load_session(UpdateWorkflow.FLOW) assert (b.session.get_status(Workflow.FLOW_INIT)) @@ -198,7 +198,7 @@ def test_clean_old_sessions(self): """ b = Bank('local') for i in range(1,5): - s = Session('alu', self.config, UpdateWorkflow.FLOW) + s = Session('pdbaa', self.config, UpdateWorkflow.FLOW) s._session['status'][Workflow.FLOW_INIT] = True b.session = s b.save_session() @@ -211,20 +211,20 @@ def test_session_reload_over(self): """ Checks a session if is not over """ - b = Bank('alu') + b = Bank('pdbaa') for i in range(1,5): - s = Session('alu', self.config, UpdateWorkflow.FLOW) + s = Session('pdbaa', self.config, UpdateWorkflow.FLOW) s._session['status'][Workflow.FLOW_INIT] = True s._session['status'][Workflow.FLOW_OVER] = True b.session = s b.save_session() - b = Bank('alu') + b = Bank('pdbaa') b.load_session(UpdateWorkflow.FLOW) assert not (b.session.get_status(Workflow.FLOW_INIT)) def test_bank_list(self): - b1 = Bank('alu') + b1 = Bank('pdbaa') b2 = Bank('local') banks = Bank.list() assert (len(banks) == 2) @@ -237,7 +237,7 @@ def test_get_release(self): """ Get release """ - b = Bank('alu') + b = Bank('pdbaa') b.load_session(UpdateWorkflow.FLOW) res = b.update() assert (b.session.get('update')) @@ -249,9 +249,9 @@ def test_get_release(self): reason='network tests disabled' ) def test_remove_session(self): - b = Bank('alu') + b = Bank('pdbaa') for i in range(1,5): - s = Session('alu', self.config, UpdateWorkflow.FLOW) + s = Session('pdbaa', self.config, UpdateWorkflow.FLOW) s._session['status'][Workflow.FLOW_INIT] = True b.session = s b.save_session() diff --git a/tests/alu.properties b/tests/pdbaa.properties similarity index 81% rename from tests/alu.properties rename to tests/pdbaa.properties index 0e729e0..b3d38c1 100644 --- a/tests/alu.properties +++ b/tests/pdbaa.properties @@ -3,11 +3,11 @@ ### Initialization ### db.fullname="alu.n : alu repeat element. alu.a : translation of alu.n repeats" -db.name=alu +db.name=pdbaa db.type=nucleic_protein -offline.dir.name=offline/ncbi/blast/alu_tmp -dir.version=ncbi/blast/alu +offline.dir.name=offline/ncbi/blast/pdbaa_tmp +dir.version=ncbi/blast/pdbaa frequency.update=0 @@ -24,12 +24,12 @@ release.file= release.regexp= release.file.compressed= -remote.files=^alu.*\.gz$ +remote.files=^pdbaa.*\.gz$ #Uncomment if you don't want to extract the data files. #no.extract=true -local.files=^alu\.(a|n).* +local.files=^pdbaa\.*$ ## Post Process ## The files should be located in the projectfiles/process directory