missing setup.py

src/xchemalign/setup.py

@@ -0,0 +1,85 @@
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+import argparse
+import math
+import os
+from pathlib import Path
+
+
+from xchemalign import utils
+
+
+class Setup:
+    def __init__(self, working_dir: Path):
+        if not working_dir:
+            self.working_dir = Path.cwd()
+        else:
+            self.working_dir = Path(working_dir)
+        self.version_dir = Path('upload-v' + str(math.floor(utils.DATA_FORMAT_VERSION)))
+        self.sym_dir = Path('upload-current')
+        self.logger = utils.Logger(logfile=self.working_dir / 'setup.log')
+        utils.LOG = self.logger
+
+    def run(self):
+        self.logger.info("Using {} as working dir".format(self.working_dir))
+        self.logger.info("Current data format version is", utils.DATA_FORMAT_VERSION)
+
+        if self._pre_flight_checks() > 1:
+            exit(1)
+        self._create()
+        self._inform()
+
+    def _pre_flight_checks(self):
+        if (self.working_dir / self.sym_dir).exists():
+            self.logger.error(
+                "Working directory",
+                self.working_dir,
+                "already seems to have been setup. Please empty it and try again",
+            )
+            return 1
+        return 0
+
+    def _create(self):
+        os.mkdir(self.working_dir / self.version_dir)
+        os.mkdir(self.working_dir / self.version_dir / 'upload_1')
+        open(self.working_dir / self.version_dir / "config.yaml", 'w').close()
+        open(self.working_dir / self.version_dir / "assemblies.yaml", 'w').close()
+        cwd = Path.cwd()
+        os.chdir(self.working_dir)
+        os.symlink(self.version_dir, self.sym_dir, target_is_directory=True)
+        os.chdir(cwd)
+
+    def _inform(self):
+        self.logger.info("Your working environment has been set up in", (self.working_dir / self.sym_dir))
+        self.logger.info("In there you will find dummy config.yaml and assemblies.yaml files")
+        self.logger.info("You will need to edit these as described in the User Guide.")
+        self.logger.info(
+            "Then you can run collator like this (omit the -d argument if you are already in "
+            + "that directory):\n      python -m xchemalign.collator -d",
+            self.working_dir,
+        )
+
+
+def main():
+    parser = argparse.ArgumentParser(description="setup")
+
+    parser.add_argument("-d", "--dir", help="Working directory")
+
+    args = parser.parse_args()
+
+    s = Setup(args.dir)
+    s.run()
+
+
+if __name__ == "__main__":
+    main()