dependency versioning (#48)

* dependency minimum versions

* lint?

* need quotes?

* another go

* readme, mypy install

.github/workflows/mypy.yml

@@ -25,6 +25,6 @@ jobs:
     - name: mypy
       run: |
         pip install mypy
-        pip install .
+        pip install '.[tests]'
         mkdir .mypy_cache
         mypy --install-types --non-interactive meteor/ test/

.github/workflows/tests.yml

@@ -26,8 +26,7 @@ jobs:
     
     - name: Test with pytest
       run: |
-        pip install pytest pytest-cov
-        pip install .
+        pip install '.[tests]'
         pytest test/
     
     - name: Upload coverage to Codecov  

README.md

@@ -16,10 +16,20 @@ Map Enhancement Tools for Ephemeral Occupancy Refinement
 
 ❗ `meteor` is currently **in beta**. We re-wrote everything recently, moving from a research code to something that can be robustly used as a tool. If you are willing to put up with a few sharp edges, it would be great if you give it a spin and then send us feedback: on how easy/not it was to use and what kinds of scientific results you obtain.
 
-Finally: a word of caution. Expect changes in the coming weeks as we stress test the code. You might want to consider this before publishing any results with `meteor` until we exit `beta`.
+Finally: a word of caution. Expect changes in the coming weeks as we stress test the code. You might want to consider this before publishing any results with `meteor` until we exit `beta`. 
 
+In that vein, for now please install the current master branch as per the following instructions. We'll have a sane
+first stable version soon, which will be deployed straight to `PyPI` and `conda-forge`. Stay posted.
+
+First, we recommend you make a new environment. For conda users,
+```
+conda create --name meteor python==3.11 --yes
+conda activate meteor
+```
+
+Then install from github,
 ```
-TODO: installation instructions
+pip install git+https://github.com/alisiafadini/meteor
 ```
 
 Once installed, you will have two command-line scripts. Ask for more info using `-h`:

meteor/scripts/compute_difference_map.py

@@ -148,9 +148,7 @@ def denoise_diffmap_according_to_mode(
         Information regarding the denoising process.
     """
     if tv_denoise_mode == WeightMode.optimize:
-        log.info(
-            "Searching for max-negentropy TV denoising weight", method="golden-section search"
-        )
+        log.info("Searching for max-negentropy TV denoising weight", method="golden-section search")
         log.info("This may take some time...")
 
         final_map, metadata = tv_denoise_difference_map(diffmap, full_output=True)

pyproject.toml

@@ -7,19 +7,18 @@ authors = [
     { name = "Thomas Lane", email = "[email protected]" }
 ]
 dependencies = [
-    "numpy",
-    "scipy",
-    "gemmi",
-    "scikit-image",
-    "reciprocalspaceship",
-    "structlog",
-    "pytest",
-    "pytest-cov",
+    "numpy >= 1.26",
+    "scipy >= 1.14.0",
+    "gemmi >= 0.6.6",
+    "scikit-image >= 0.24.0",
+    "reciprocalspaceship >= 1.0.2",
+    "structlog >= 24.4.0",
 ]
 
 [project.optional-dependencies]
-dev = [
-    "pre-commit",
+tests = [
+    "pytest",
+    "pytest-cov",
 ]
 
 [build-system]