simstack 0.2.0__py3-none-any.whl

simstack-0.2.0.dist-info/METADATA

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+Metadata-Version: 2.4
+Name: simstack
+Version: 0.2.0
+Summary: A python based workflow engineering platform with a react-js UI
+Author-email: Wolfgang Wenzel <wolfgang.wenzel@kit.edu>, Timo Strunk <timo.strunk@nanomatch.de>
+License: MIT
+Project-URL: Homepage, https://gitlab.kit.edu/kit/ag_wenzel/simstack-model/
+Requires-Python: >=3.12
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: odmantic<2,>=1.0.2
+Requires-Dist: cloudpickle<4,>=3.1.1
+Requires-Dist: coolname<3,>=2.2.0
+Requires-Dist: nest-asyncio<2,>=1.6.0
+Requires-Dist: numpy>=2.3.0
+Requires-Dist: pandas>=2.3.3
+Dynamic: license-file
+
+## 1. Install Simstack II — 3-step lightning setup ⚡️
+
+> **Goal:** create an isolated **`simstack`** environment, pull the model code, and satisfy every dependency in a single
+> coffee break.
+
+| What you’ll do                          | Why it matters                                     |
+|-----------------------------------------|----------------------------------------------------|
+| 1 Create a project specific environment | Keeps your system Python pristine                  |
+| 2 Install simstack                      |
+| 3 Clone relevant simstack base packages | Gives you ready-made tasks, sample data, and tests |
+
+---
+
+### Step 1 — Spin up the `simstack` environment 🐍
+
+Choose your favorite Python **env manager**
+
+The most modern managers are **pixi** for conda-style and **uv** for pip-style.
+
+<details open>
+<summary><strong>⬤ Recommended – Mamba (10× faster)</strong></summary>
+
+Install **Mamba** if you don’t have it
+See mamba [documentation](https://mamba.readthedocs.io/en/latest/) for Windows, Linux and macOS.
+
+```bash
+mamba create -n simstack python=3.12 -y
+mamba activate simstack
+```
+</details>
+
+<details>
+<summary><strong>⬤ micromamba – single-file binary</strong></summary>
+
+```bash
+micromamba create -n simstack python=3.12 -y
+micromamba activate simstack
+```
+</details>
+
+<details>
+<summary><strong>⬤ Classic conda</strong></summary>
+
+```bash
+conda create -n simstack python=3.12 -y
+conda activate simstack
+```
+</details>
+
+**Heads-up**: Simstack II works with Python ≥ 3.12 (CPython 64-bit).
+Older versions (<3.12) may miss tomllib support and fail at runtime.
+
+### Step 2 — Install simstack 📦
+
+```bash
+# activate the (simstack) env
+python -m pip install --upgrade pip
+pip install simstack
+
+Just type `tree` in the terminal, if the **installation** succeeds, you should see a directory structure like the folder tree shown below.
+
+### Step 3 — Clone subrepos for existing simstack packages 📦
+
+```bash
+# activate the (simstack) env
+python -m pip install --upgrade pip
+pip install simstack
+
+Just type `tree` in the terminal, if the **installation** succeeds, you should see a directory structure like the folder tree shown below.
+
+
+
+### Step 2 — Install dependencies 📦
+
+```bash
+# activate the (simstack) env
+python -m pip install --upgrade pip
+pip install simstack
+
+Just type `tree` in the terminal, if the **installation** succeeds, you should see a directory structure like the folder tree shown below.
+
+
+
+
+
+## 2. Configure Simstack II with `simstack.toml` ⚙️
+
+Simstack II reads a single **TOML** file (`simstack.toml`) to learn
+
+* which **resources** (local & remote) exist,
+* how to reach your **MongoDB** backend,
+* and where each host should place logs / artifacts.
+
+> **Where should the file live?**
+> Save it next in the folder simstack-model in both your local and HPC accounts.
+> The CLI searches those paths automatically.
+
+### 2.1 Minimal template
+
+```toml
+#######################################
+# Global / shared parameters
+#######################################
+[parameters.common]
+resources        = ["local", "int-nano", "horeka", "justus", "self", "exchange", "uploads"]
+database         = "celso_data"                    # default DB
+test_database    = "celso_test_data"               # used by `simstack selftest`
+connection_string = "mongodb://<user>:<pass>@<host>:27017/"  # ⬚ change!
+
+#######################################
+# Host-specific overrides
+#######################################
+# 1) Your own machine --------------------------------
+[parameters.local]
+ssh-key     = "~/.ssh/id_rsa"                      # private key
+resource    = "local"                              # → maps to runners.local
+workdir     = "~/simstack/workflows"               # absolute path
+python_path = ["~/simstack/simstack-model",
+               "~/simstack/simstack-model/src"]
+
+# 2) Remote upload node -----------------------------
+[parameters.uploads]
+ssh-key     = "~/.ssh/id_rsa"
+resource    = "self"
+workdir     = "~/simstack/workflows"
+python_path = ["~/simstack/simstack-model",
+               "~/simstack/simstack-model/src"]
+
+# 3) Example HPC login node -------------------------
+[parameters.int-nano]
+ssh-key            = "~/.ssh/id_rsa"
+workdir            = "/home/<user>/simstack"
+python_path        = ["/home/<user>/simstack/simstack-model",
+                      "/home/<user>/simstack/simstack-model/src"]
+environment_start  = "mamba activate simstack"  # run before each task
+
+#######################################
+# Internal web-server (rarely touched)
+#######################################
+[server]
+port        = 8000
+SECRET_KEY  = "<32-byte hex or env-var>"           # ⬚ never commit real keys
+upload_dir  = "/srv/simstack/uploads"              # Windows paths OK too
+
+#######################################
+# Canonical DNS names for hosts
+#######################################
+[hosts]
+local    = "localhost"
+int-nano = "int-nano.int.kit.edu"
+justus   = "justus.int.kit.edu"
+horeka   = "horeka.int.kit.edu"
+
+#######################################
+# Directed data routes
+#######################################
+[[routes]]
+source = "local"     # where the artifact lives
+target = "int-nano"  # where you want it
+host   = "local"     # node that **pushes** the data
+
+[[routes]]
+source = "int-nano"
+target = "local"
+host   = "local"
+
+# …repeat as needed
+```
+
+## 3 Prepare *PYTHONPATH* locally & on every HPC account 📂
+
+Add **both** the project root and its `src/` directory to `PYTHONPATH` so every Simstack II task can resolve imports no matter where it runs.
+
+### 3.1 Create a helper script once (call it `set_pythonpath.sh`):
+
+   ```bash
+   #!/usr/bin/env bash
+   # -----------------------------
+   # Adds the current repo + src/ to PYTHONPATH
+   # Call with:  source set_pythonpath.sh
+   # -----------------------------
+   this_dir="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
+   export PYTHONPATH="$this_dir:$this_dir/src${PYTHONPATH+:$PYTHONPATH}"
+   echo "PYTHONPATH = $PYTHONPATH"
+   ```
+
+### 3.2 Make it executable & load it whenever you open a new shell:
+
+```bash
+chmod +x set_pythonpath.sh        # one-time
+source /path/to/set_pythonpath.sh # every session, or add to ~/.bashrc
+```
+
+### 3.3 Copy the script to each HPC account (e.g. int-nano, horeka, …):
+
+```bash
+scp set_pythonpath.sh user@int-nano.int.kit.edu:~/simstack/
+```
+
+## 4. Ready, Set, Workflow! 🏁
+
+**Mission**: prime Simstack II so your very first workflow launches without a hiccup—DB seeded, nodes known, runner humming.
+
+### 🥇 Step 1 — Initialize the database
+
+Simstack keeps its model and node catalogue in MongoDB. Populate (or refresh) the tables whenever you pull a new commit:
+
+```python!
+# from the repo root
+cd src/simstack/utils        # ⇢ utility scripts live here
+python model_table.py       # 🚀 inserts/updates the “Models” collection
+python node_table.py         # 🚀 inserts/updates the “Nodes”  collection
+```
+### 🥈 Step 2 — Re‑register nodes (WaNos) 🔄
+
+Any time you change a **node definition**—be it locally or on an HPC cluster—you must (re)announce it to the control plane:
+
+```python!
+# ▸ Local workstation
+python src/simstack/core/node.py  # instantaneous
+
+# ▸ On int‑nano (or another cluster head node)
+ssh user@int-nano.int.kit.edu
+python ~/simstack/src/simstack/core/node.py
+```
+
+Why **WaNos**?  Workflow Aware Nodes—nodes that tell Simstack exactly what they’re capable of.
+
+### 🥉 Step 3 — Fire up the runner on int‑nano 🚀
+
+```python!
+ssh user@int-nano.int.kit.edu           # 1️⃣ log in
+source ~/simstack/set_pythonpath.sh  # 2️⃣ expose src/ to PYTHONPATH
+python src/simstack/core/runner.py --resource int-nano  # 3️⃣ start runner
+```
+
+You should see something like:
+```bash!
+2025-04-24 11:26:58 - ConfigReader - INFO - Initializing ConfigReader with resource: local on database celso_data
+2025-04-24 11:26:58 - ConfigReader - INFO - workdir: /home/celso/Desktop/Project/KIT/simstack/Files/simstack_workflows
+```
+
+The runner now listens for jobs assigned to the int-nano resource and inherits the correct PYTHONPATH so your code imports flawlessly.
+
+```bash!
+[Runner‑int‑nano] ⚡️  connected to broker
+[Runner‑int‑nano] 💤  waiting for tasks (Ctrl‑C to exit)
+```
+
+### 5. Hands‑On: binary_operations.py 🧮
+
+Your environment is up, let's run a real Simstack workflow on your local machine.
+
+### 5.1 What the code does
+
+```python!
+# simplified excerpt
+a, b, c = 5, 10, 2          # sample inputs
+add_result      = a + b      # → 15
+multiply_result = add_result * c  # → 30
+print(multiply_result)
+```
+*Under the hood it uses the FloatData ODM model so the result is automatically stored in MongoDB with an ObjectId.*
+
+### 5.2 Run it 🚀
+
+```bash!
+# stay inside your (simstack) env
+cd simstack-model/examples   # 1️⃣ go to examples directory
+python binary_operations.py  # 2️⃣ execute workflow script
+```
+Expected terminal output (the ObjectId will differ):
+
+```bash!
+id=ObjectId('680f3c149f39611649075d6a') value=30.0
+```
+
+🎉 **Congrats!** You’ve just:
+
+ **1.** Sent inputs through Simstack’s data‑model layer
+
+ **2.** Executed the adder ➜ multiplier chain
+
+ **3.** Persisted the final result in your configured MongoDB instance
+
+Try changing the numbers in AddMultiplyInput(a, b, c) and re‑running to see different results. Feel free to explore other examples in the same folder or craft your own!
+
+### 5.4 — Run *node_example.py* on **int-nano** via Slurm 🏎️💨
+
+> **Mission:** Run `node_example.py` workflow in **int-nano** HPC cluster and let Simstack II generate & submit the Slurm job for you.
+---
+
+#### 🔑 Prerequisites
+
+1. **Runner up & listening on int-nano**
+   ```bash
+   # on the int-nano login node
+   ssh user@int-nano.int.kit.edu
+   source ~/simstack/set_pythonpath.sh     # expose src/ to PYTHONPATH
+   python src/simstack/core/runner.py --resource int-nano
+
+Leave this terminal open—your runner will watch the message broker for tasks targeting int-nano.
+
+`node_example.py` available on your workstation (it lives in simstack-model/examples).
+
+Slurm access on int-nano (the runner will create and submit the sbatch scripts for you).
+
+### 🚀 Launch the workflow from your local machine
+
+```python!
+# still in (simstack) and inside simstack-model/examples on the local machine
+python node_example.py
+```
+
+That single command does three things behind the scenes:
+
+1. **Creates a task document** in MongoDB with resource="int-nano", queue="slurm".
+
+2. **Signals the int-nano runner**, which in turn
+
+* auto-generates an `id_num.err`, `id_num.out`, and `slurm_script.sh` file inside <workdir>/adder/ (see your simstack.toml)
+* submits it with sbatch.
+
+3. **Streams status** back to your local terminal until completion.
+
+### 🖥️ Expected local console output
+
+```bash!
+task_id: 680f4ac265bb513834eeb92a created in read_db Task adder with 680f4ac265bb513834eeb92a is waiting for results
+2025-04-28 11:30:47 - simstack.core.node - INFO - Task adder with task_id: 680f4ac265bb513834eeb92a completed remotely
+2025-04-28 11:30:47 - simstack.core.node - INFO - Task adder with task_id: 680f4ac265bb513834eeb92a found with status TaskStatus.COMPLETED
+2025-04-28 11:30:47 - simstack.core.node - INFO - Task adder with task_id: 680f4ac265bb513834eeb92a loaded outputs
+```
+
+Once you see TaskStatus.COMPLETED, the Slurm job finished on int-nano and the result document was synced back to your MongoDB.
+
+Now you’ve successfully:
+
+* Spun up a remote runner on int-nano.
+* Queued a Slurm job without writing a single sbatch file yourself.
+* Retrieved the output transparently through Simstack II’s data layer.
+
+Tweak the numbers in the script, re-run, and watch new adder.sbatch files—and fresh Slurm job-IDs—appear in your adder/ folder. Enjoy the speed-up! ⚡️

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+simstack/util/module_path_checker.py,sha256=9NJHtLIACrbFVC5stMlskKb2et2rUqccoL8aDwkfItI,1415
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+simstack/util/project_root_finder.py,sha256=0ZH72NrfvjDpCQxB6TTyjCQMv2X_BlzbAALFBdsYPaE,1215
+simstack/util/queue_watcher.py,sha256=5I2zI5Pofw9tXt832Etz6dTfJkzYEVg-SgCAK6Ce6o8,8841
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+simstack/util/safe_code_executor.py,sha256=1F9WZWW3qby3zWdHHVi2cb6NG9ZeZWL_3pizTF1OHd0,6467
+simstack/util/sample_config.py,sha256=Q1cwrzoPghV5ff3VRdN1YhkLirixXlf6OGjaR06JFdI,3541
+simstack/util/sensitive_content_filter.py,sha256=RHeLtBAPrwKYUL2fn9HzjjHw_YlDkNhRdi2ISw-8a1g,1695
+simstack/util/setup_logging.py,sha256=AYI17k8zBMCSglhdwio-1BsaUdWs3N3S4euvOupEpD0,1629
+simstack/util/submit_to_watchdog.py,sha256=R6cH4R2KY8UKyjcn4u7Z6u0LxH50NYeS7LXlRN85cpM,2937
+simstack/util/ui_tools.py,sha256=iSO6z6kNnJZQ6kqbKAv8pjuUB4hde95iQpynnfvE9js,7109
+simstack-0.2.0.dist-info/licenses/LICENSE,sha256=H5wo5y-DywFxjVbYr5YHwNpTTfI1eh0ztz-xQwU92mw,1080
+simstack-0.2.0.dist-info/METADATA,sha256=zmDQyyz6ZOI1kkRLlHs8VmkELI-WJ71qFWz5bt-hYgo,12478
+simstack-0.2.0.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+simstack-0.2.0.dist-info/entry_points.txt,sha256=779MFBByo0AjijU-rFcYeYaQLY45TmKEnUm6-DoAgqg,439
+simstack-0.2.0.dist-info/top_level.txt,sha256=-tfARSqXVVKmSYiL_cknn5ZEvohMhvoWXOavCmWFN9A,9
+simstack-0.2.0.dist-info/RECORD,,

simstack-0.2.0.dist-info/WHEEL

@@ -0,0 +1,5 @@
+Wheel-Version: 1.0
+Generator: setuptools (80.9.0)
+Root-Is-Purelib: true
+Tag: py3-none-any
+

simstack-0.2.0.dist-info/entry_points.txt

@@ -0,0 +1,10 @@
+[console_scripts]
+create_model_table = simstack.core.model_table:create_model_table_main
+create_node_table = simstack.core.node_table:create_node_table_main
+run_node = simstack.core.run_node:run_node_main
+simstack_runner = simstack.core.runner:runner_main
+simstack_write_sample_config = simstack.util.sample_config:sample_config_writer_entrypoint
+
+[simstack.modules]
+applicatio_modules = simstack.methods
+example_modules = simstack.models

simstack-0.2.0.dist-info/licenses/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2025 Wolfgang Wenzel
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the “Software”), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED “AS IS”, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.

simstack-0.2.0.dist-info/top_level.txt

@@ -0,0 +1 @@
+simstack