Fix (#15)

* Fix help message

* Add missing dependency: scipy

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "hotaru"
-version = "3.3.0"
+version = "3.3.1"
 description = "High performance Optimizer to extract spike Timing And cell location from calcium imaging data via lineaR impUlse"
 license = "GPL-3.0-only"
 authors = ["TAKEKAWA Takashi <[email protected]>"]
@@ -14,6 +14,7 @@ tensorflow = "^2.3.1"
 tifffile = "^2020.5.11"
 matplotlib = "^3.2.1"
 cleo = "^0.8.1"
+scipy = "^1.5.4"
 
 [tool.poetry.dev-dependencies]
 pytest = "^5.4.1"

requirements.txt

@@ -303,6 +303,32 @@ requests-oauthlib==1.3.0 \
 rsa==4.6; python_version >= "3.5" \
     --hash=sha256:23778f5523461cf86ae075f9482a99317f362bca752ae57cb118044066f4026f \
     --hash=sha256:109ea5a66744dd859bf16fe904b8d8b627adafb9408753161e766a92e7d681fa
+scipy==1.5.4 \
+    --hash=sha256:4f12d13ffbc16e988fa40809cbbd7a8b45bc05ff6ea0ba8e3e41f6f4db3a9e47 \
+    --hash=sha256:a254b98dbcc744c723a838c03b74a8a34c0558c9ac5c86d5561703362231107d \
+    --hash=sha256:368c0f69f93186309e1b4beb8e26d51dd6f5010b79264c0f1e9ca00cd92ea8c9 \
+    --hash=sha256:4598cf03136067000855d6b44d7a1f4f46994164bcd450fb2c3d481afc25dd06 \
+    --hash=sha256:e98d49a5717369d8241d6cf33ecb0ca72deee392414118198a8e5b4c35c56340 \
+    --hash=sha256:65923bc3809524e46fb7eb4d6346552cbb6a1ffc41be748535aa502a2e3d3389 \
+    --hash=sha256:9ad4fcddcbf5dc67619379782e6aeef41218a79e17979aaed01ed099876c0e62 \
+    --hash=sha256:f87b39f4d69cf7d7529d7b1098cb712033b17ea7714aed831b95628f483fd012 \
+    --hash=sha256:25b241034215247481f53355e05f9e25462682b13bd9191359075682adcd9554 \
+    --hash=sha256:fa789583fc94a7689b45834453fec095245c7e69c58561dc159b5d5277057e4c \
+    --hash=sha256:d6d25c41a009e3c6b7e757338948d0076ee1dd1770d1c09ec131f11946883c54 \
+    --hash=sha256:2c872de0c69ed20fb1a9b9cf6f77298b04a26f0b8720a5457be08be254366c6e \
+    --hash=sha256:e360cb2299028d0b0d0f65a5c5e51fc16a335f1603aa2357c25766c8dab56938 \
+    --hash=sha256:3397c129b479846d7eaa18f999369a24322d008fac0782e7828fa567358c36ce \
+    --hash=sha256:168c45c0c32e23f613db7c9e4e780bc61982d71dcd406ead746c7c7c2f2004ce \
+    --hash=sha256:213bc59191da2f479984ad4ec39406bf949a99aba70e9237b916ce7547b6ef42 \
+    --hash=sha256:634568a3018bc16a83cda28d4f7aed0d803dd5618facb36e977e53b2df868443 \
+    --hash=sha256:b03c4338d6d3d299e8ca494194c0ae4f611548da59e3c038813f1a43976cb437 \
+    --hash=sha256:3d5db5d815370c28d938cf9b0809dade4acf7aba57eaf7ef733bfedc9b2474c4 \
+    --hash=sha256:6b0ceb23560f46dd236a8ad4378fc40bad1783e997604ba845e131d6c680963e \
+    --hash=sha256:ed572470af2438b526ea574ff8f05e7f39b44ac37f712105e57fc4d53a6fb660 \
+    --hash=sha256:8c8d6ca19c8497344b810b0b0344f8375af5f6bb9c98bd42e33f747417ab3f57 \
+    --hash=sha256:d84cadd7d7998433334c99fa55bcba0d8b4aeff0edb123b2a1dfcface538e474 \
+    --hash=sha256:cc1f78ebc982cd0602c9a7615d878396bec94908db67d4ecddca864d049112f2 \
+    --hash=sha256:4a453d5e5689de62e5d38edf40af3f17560bfd63c9c5bd228c18c1f99afa155b
 six==1.15.0 \
     --hash=sha256:8b74bedcbbbaca38ff6d7491d76f2b06b3592611af620f8426e82dddb04a5ced \
     --hash=sha256:30639c035cdb23534cd4aa2dd52c3bf48f06e5f4a941509c8bafd8ce11080259

src/hotaru/console/config.py

@@ -18,8 +18,8 @@ class ConfigCommand(Command):
         _option('name', None, ''),
         _option('pbar', None, ''),
 
-        _option('imgs-file'),
-        _option('mask-type'),
+        _option('imgs-file', None, ''),
+        _option('mask-type', None, ''),
 
         _option('tau-rise', None, 'time constant of calicum raise (sec)'),
         _option('tau-fall', None, 'time constant of calcium fall (sec)'),